Ben Bolstad
| Snapshot Date: 2025-11-24 13:45 -0500 (Mon, 24 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: RELEASE_3_22 |
| git_last_commit: d2ce144 |
| git_last_commit_date: 2025-10-29 09:58:55 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-27 12:04 -0500 (Thu, 27 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4876 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4656 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4602 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 257/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.74.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BufferedMatrix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrix.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BufferedMatrix |
| Version: 1.74.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BufferedMatrix_1.74.0.tar.gz |
| StartedAt: 2025-11-25 17:53:02 -0500 (Tue, 25 Nov 2025) |
| EndedAt: 2025-11-25 17:54:00 -0500 (Tue, 25 Nov 2025) |
| EllapsedTime: 57.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BufferedMatrix_1.74.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.74.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BufferedMatrix’ can be installed ... WARNING
Found the following significant warnings:
doubleBufferedMatrix.c:1580:7: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
See ‘/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) BufferedMatrix-class.Rd:209: Lost braces; missing escapes or markup?
209 | $x^{power}$ elementwise of the matrix
| ^
prepare_Rd: createBufferedMatrix.Rd:26: Dropping empty section \keyword
prepare_Rd: createBufferedMatrix.Rd:17-18: Dropping empty section \details
prepare_Rd: createBufferedMatrix.Rd:15-16: Dropping empty section \value
prepare_Rd: createBufferedMatrix.Rd:19-20: Dropping empty section \references
prepare_Rd: createBufferedMatrix.Rd:21-22: Dropping empty section \seealso
prepare_Rd: createBufferedMatrix.Rd:23-24: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘Rcodetesting.R’
Running ‘c_code_level_tests.R’
Running ‘objectTesting.R’
Running ‘rawCalltesting.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.74.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RBufferedMatrix.c -o RBufferedMatrix.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c:1580:7: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
if (!(Matrix->readonly) & setting){
^ ~
doubleBufferedMatrix.c:1580:7: note: add parentheses after the '!' to evaluate the bitwise operator first
if (!(Matrix->readonly) & setting){
^
( )
doubleBufferedMatrix.c:1580:7: note: add parentheses around left hand side expression to silence this warning
if (!(Matrix->readonly) & setting){
^
( )
doubleBufferedMatrix.c:3327:12: warning: unused function 'sort_double' [-Wunused-function]
static int sort_double(const double *a1,const double *a2){
^
2 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init_package.c -o init_package.o
clang -arch arm64 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘rowMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘rowSums’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colSums’ in package ‘BufferedMatrix’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘BufferedMatrix’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘BufferedMatrix’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BufferedMatrix)
BufferedMatrix.Rcheck/tests/c_code_level_tests.Rout
R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix", "BufferedMatrix", .libPaths());.C("dbm_c_tester",integer(1))
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
Adding Additional Column
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000
Reassigning values
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 3
Buffer Cols: 3
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Activating Row Buffer
In row mode: 1
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Squaring Last Column
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
5.000000 10.000000 15.000000 20.000000 25.000000 900.000000
Square rooting Last Row, then turing off Row Buffer
In row mode: 0
Checking on value that should be not be in column buffer2.236068
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
2.236068 3.162278 3.872983 4.472136 5.000000 30.000000
Single Indexing. Assign each value its square
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Resizing Buffers Smaller
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Activating Row Mode.
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
Activating ReadOnly Mode.
The results of assignment is: 0
Printing matrix reversed.
900.000000 625.000000 400.000000 225.000000 100.000000 25.000000
841.000000 576.000000 361.000000 196.000000 81.000000 16.000000
784.000000 529.000000 324.000000 169.000000 64.000000 9.000000
729.000000 484.000000 289.000000 144.000000 49.000000 -30.000000
676.000000 441.000000 256.000000 121.000000 -20.000000 -10.000000
[[1]]
[1] 0
>
> proc.time()
user system elapsed
0.344 0.112 0.572
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
>
> ### this is used to control how many repetitions in something below
> ### higher values result in more checks.
> nreps <-100 ##20000
>
>
> ## test creation and some simple assignments and subsetting operations
>
> ## first on single elements
> tmp <- createBufferedMatrix(1000,10)
>
> tmp[10,5]
[1] 0
> tmp[10,5] <- 10
> tmp[10,5]
[1] 10
> tmp[10,5] <- 12.445
> tmp[10,5]
[1] 12.445
>
>
>
> ## now testing accessing multiple elements
> tmp2 <- createBufferedMatrix(10,20)
>
>
> tmp2[3,1] <- 51.34
> tmp2[9,2] <- 9.87654
> tmp2[,1:2]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[,-(3:20)]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 51.34 0 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
> tmp2[-3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0
[5,] 0 0 0 0 0 0 0
[6,] 0 0 0 0 0 0 0
[7,] 0 0 0 0 0 0 0
[8,] 0 0 0 0 0 0 0
[9,] 0 0 0 0 0 0 0
> tmp2[2,1:3]
[,1] [,2] [,3]
[1,] 0 0 0
> tmp2[3:9,1:3]
[,1] [,2] [,3]
[1,] 51.34 0.00000 0
[2,] 0.00 0.00000 0
[3,] 0.00 0.00000 0
[4,] 0.00 0.00000 0
[5,] 0.00 0.00000 0
[6,] 0.00 0.00000 0
[7,] 0.00 9.87654 0
> tmp2[-4,-4]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 51.34 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0.00 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19]
[1,] 0 0 0 0 0 0
[2,] 0 0 0 0 0 0
[3,] 0 0 0 0 0 0
[4,] 0 0 0 0 0 0
[5,] 0 0 0 0 0 0
[6,] 0 0 0 0 0 0
[7,] 0 0 0 0 0 0
[8,] 0 0 0 0 0 0
[9,] 0 0 0 0 0 0
>
> ## now testing accessing/assigning multiple elements
> tmp3 <- createBufferedMatrix(10,10)
>
> for (i in 1:10){
+ for (j in 1:10){
+ tmp3[i,j] <- (j-1)*10 + i
+ }
+ }
>
> tmp3[2:4,2:4]
[,1] [,2] [,3]
[1,] 12 22 32
[2,] 13 23 33
[3,] 14 24 34
> tmp3[c(-10),c(2:4,2:4,10,1,2,1:10,10:1)]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 11 21 31 11 21 31 91 1 11 1 11 21 31
[2,] 12 22 32 12 22 32 92 2 12 2 12 22 32
[3,] 13 23 33 13 23 33 93 3 13 3 13 23 33
[4,] 14 24 34 14 24 34 94 4 14 4 14 24 34
[5,] 15 25 35 15 25 35 95 5 15 5 15 25 35
[6,] 16 26 36 16 26 36 96 6 16 6 16 26 36
[7,] 17 27 37 17 27 37 97 7 17 7 17 27 37
[8,] 18 28 38 18 28 38 98 8 18 8 18 28 38
[9,] 19 29 39 19 29 39 99 9 19 9 19 29 39
[,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
[1,] 41 51 61 71 81 91 91 81 71 61 51 41
[2,] 42 52 62 72 82 92 92 82 72 62 52 42
[3,] 43 53 63 73 83 93 93 83 73 63 53 43
[4,] 44 54 64 74 84 94 94 84 74 64 54 44
[5,] 45 55 65 75 85 95 95 85 75 65 55 45
[6,] 46 56 66 76 86 96 96 86 76 66 56 46
[7,] 47 57 67 77 87 97 97 87 77 67 57 47
[8,] 48 58 68 78 88 98 98 88 78 68 58 48
[9,] 49 59 69 79 89 99 99 89 79 69 59 49
[,26] [,27] [,28] [,29]
[1,] 31 21 11 1
[2,] 32 22 12 2
[3,] 33 23 13 3
[4,] 34 24 14 4
[5,] 35 25 15 5
[6,] 36 26 16 6
[7,] 37 27 17 7
[8,] 38 28 18 8
[9,] 39 29 19 9
> tmp3[-c(1:5),-c(6:10)]
[,1] [,2] [,3] [,4] [,5]
[1,] 6 16 26 36 46
[2,] 7 17 27 37 47
[3,] 8 18 28 38 48
[4,] 9 19 29 39 49
[5,] 10 20 30 40 50
>
> ## assignment of whole columns
> tmp3[,1] <- c(1:10*100.0)
> tmp3[,1:2] <- tmp3[,1:2]*100
> tmp3[,1:2] <- tmp3[,2:1]
> tmp3[,1:2]
[,1] [,2]
[1,] 1100 1e+04
[2,] 1200 2e+04
[3,] 1300 3e+04
[4,] 1400 4e+04
[5,] 1500 5e+04
[6,] 1600 6e+04
[7,] 1700 7e+04
[8,] 1800 8e+04
[9,] 1900 9e+04
[10,] 2000 1e+05
>
>
> tmp3[,-1] <- tmp3[,1:9]
> tmp3[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1100 1100 1e+04 21 31 41 51 61 71 81
[2,] 1200 1200 2e+04 22 32 42 52 62 72 82
[3,] 1300 1300 3e+04 23 33 43 53 63 73 83
[4,] 1400 1400 4e+04 24 34 44 54 64 74 84
[5,] 1500 1500 5e+04 25 35 45 55 65 75 85
[6,] 1600 1600 6e+04 26 36 46 56 66 76 86
[7,] 1700 1700 7e+04 27 37 47 57 67 77 87
[8,] 1800 1800 8e+04 28 38 48 58 68 78 88
[9,] 1900 1900 9e+04 29 39 49 59 69 79 89
[10,] 2000 2000 1e+05 30 40 50 60 70 80 90
>
> tmp3[,1:2] <- rep(1,10)
> tmp3[,1:2] <- rep(1,20)
> tmp3[,1:2] <- matrix(c(1:5),1,5)
>
> tmp3[,-c(1:8)] <- matrix(c(1:5),1,5)
>
> tmp3[1,] <- 1:10
> tmp3[1,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
> tmp3[-1,] <- c(1,2)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 2 1 2 1 2 1 2 1 2 1
[10,] 1 2 1 2 1 2 1 2 1 2
> tmp3[-c(1:8),] <- matrix(c(1:5),1,5)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 1 3 5 2 4 1 3 5 2 4
[10,] 2 4 1 3 5 2 4 1 3 5
>
>
> tmp3[1:2,1:2] <- 5555.04
> tmp3[-(1:2),1:2] <- 1234.56789
>
>
>
> ## testing accessors for the directory and prefix
> directory(tmp3)
[1] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests"
> prefix(tmp3)
[1] "BM"
>
> ## testing if we can remove these objects
> rm(tmp, tmp2, tmp3)
> gc()
used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
Ncells 480695 25.7 1056201 56.5 NA 634425 33.9
Vcells 890553 6.8 8388608 64.0 65536 2109045 16.1
>
>
>
>
> ##
> ## checking reads
> ##
>
> tmp2 <- createBufferedMatrix(10,20)
>
> test.sample <- rnorm(10*20)
>
> tmp2[1:10,1:20] <- test.sample
>
> test.matrix <- matrix(test.sample,10,20)
>
> ## testing reads
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Tue Nov 25 17:53:28 2025"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Tue Nov 25 17:53:28 2025"
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
>
>
> RowMode(tmp2)
<pointer: 0x60000300c480>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Tue Nov 25 17:53:32 2025"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Tue Nov 25 17:53:34 2025"
>
> ColMode(tmp2)
<pointer: 0x60000300c480>
>
>
>
> ### Now testing assignments
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+
+ new.data <- rnorm(20)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,] <- new.data
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ new.data <- rnorm(10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(25),5,5)
+ tmp2[which.row,which.col] <- new.data
+ test.matrix[which.row,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ prev.col <- which.col
+ }
>
>
>
>
> ###
> ###
> ### testing some more functions
> ###
>
>
>
> ## duplication function
> tmp5 <- duplicate(tmp2)
>
> # making sure really did copy everything.
> tmp5[1,1] <- tmp5[1,1] +100.00
>
> if (tmp5[1,1] == tmp2[1,1]){
+ stop("Problem with duplication")
+ }
>
>
>
>
> ### testing elementwise applying of functions
>
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 100.5030733 -0.16621784 -0.7442281176 -1.1568425
[2,] 0.8064573 -0.47212322 0.0008599425 -1.2144727
[3,] 0.1497868 -0.02247619 -1.0521343386 -0.5756494
[4,] 0.5628168 -1.26946318 0.0460375588 0.3108581
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 100.5030733 0.16621784 0.7442281176 1.1568425
[2,] 0.8064573 0.47212322 0.0008599425 1.2144727
[3,] 0.1497868 0.02247619 1.0521343386 0.5756494
[4,] 0.5628168 1.26946318 0.0460375588 0.3108581
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 10.0251221 0.4076982 0.86268657 1.0755661
[2,] 0.8980297 0.6871122 0.02932478 1.1020312
[3,] 0.3870230 0.1499206 1.02573600 0.7587156
[4,] 0.7502111 1.1267046 0.21456365 0.5575465
>
> my.function <- function(x,power){
+ (x+5)^power
+ }
>
> ewApply(tmp5,my.function,power=2)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 225.75429 29.24320 34.37109 36.91250
[2,] 34.78675 32.34325 25.29411 37.23478
[3,] 29.02002 26.52168 36.30949 33.16281
[4,] 33.06493 37.53651 27.19167 30.88632
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x600003010120>
> exp(tmp5)
<pointer: 0x600003010120>
> log(tmp5,2)
<pointer: 0x600003010120>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 469.878
> Min(tmp5)
[1] 52.64637
> mean(tmp5)
[1] 73.04306
> Sum(tmp5)
[1] 14608.61
> Var(tmp5)
[1] 867.4771
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 91.91633 69.29361 67.50036 72.27415 69.51373 71.33875 71.35195 71.53548
[9] 71.88667 73.81962
> rowSums(tmp5)
[1] 1838.327 1385.872 1350.007 1445.483 1390.275 1426.775 1427.039 1430.710
[9] 1437.733 1476.392
> rowVars(tmp5)
[1] 7990.22768 86.28743 78.24580 94.84344 91.82144 44.82994
[7] 68.70438 60.47470 58.79530 65.13045
> rowSd(tmp5)
[1] 89.388073 9.289103 8.845665 9.738760 9.582351 6.695517 8.288810
[8] 7.776548 7.667810 8.070344
> rowMax(tmp5)
[1] 469.87799 86.70444 82.48503 94.10051 94.01837 82.80534 91.99447
[8] 83.41669 89.26876 89.40904
> rowMin(tmp5)
[1] 56.37239 52.64637 55.20141 56.59591 56.67122 59.93252 58.26414 53.73983
[9] 53.30397 55.29035
>
> colMeans(tmp5)
[1] 111.99303 71.35430 71.89059 71.07375 69.87386 70.55622 68.76936
[8] 71.28381 71.40024 69.58114 71.40622 75.40983 71.85651 71.39384
[15] 72.09036 67.82502 69.76193 70.85989 74.00388 68.47751
> colSums(tmp5)
[1] 1119.9303 713.5430 718.9059 710.7375 698.7386 705.5622 687.6936
[8] 712.8381 714.0024 695.8114 714.0622 754.0983 718.5651 713.9384
[15] 720.9036 678.2502 697.6193 708.5989 740.0388 684.7751
> colVars(tmp5)
[1] 15872.49108 108.27052 132.97217 48.20997 56.96864 119.47337
[7] 44.53562 71.05330 68.74984 29.56519 84.95239 33.82408
[13] 82.00065 158.18078 63.69476 30.33556 69.00881 87.72166
[19] 93.96111 85.72141
> colSd(tmp5)
[1] 125.986075 10.405312 11.531356 6.943340 7.547757 10.930387
[7] 6.673501 8.429312 8.291552 5.437388 9.216962 5.815848
[13] 9.055421 12.576994 7.980900 5.507772 8.307154 9.365984
[19] 9.693354 9.258586
> colMax(tmp5)
[1] 469.87799 86.03539 84.30554 82.80534 82.39391 91.99447 77.69016
[8] 82.48503 87.50260 78.28490 86.70444 82.86622 85.19838 94.10051
[15] 88.57629 76.01074 79.68899 83.75260 89.26876 85.69660
> colMin(tmp5)
[1] 60.40136 55.20141 52.64637 61.92950 60.19377 56.37239 55.29035 53.73983
[9] 57.94584 62.23904 56.21127 66.43507 61.07632 59.93252 56.67122 58.49981
[17] 55.86283 53.30397 55.48988 56.33974
>
>
> ### setting a random element to NA and then testing with na.rm=TRUE or na.rm=FALSE (The default)
>
>
> which.row <- sample(1:10,1,replace=TRUE)
> which.col <- sample(1:20,1,replace=TRUE)
>
> tmp5[which.row,which.col] <- NA
>
> Max(tmp5)
[1] NA
> Min(tmp5)
[1] NA
> mean(tmp5)
[1] NA
> Sum(tmp5)
[1] NA
> Var(tmp5)
[1] NA
>
> rowMeans(tmp5)
[1] 91.91633 69.29361 67.50036 72.27415 69.51373 NA 71.35195 71.53548
[9] 71.88667 73.81962
> rowSums(tmp5)
[1] 1838.327 1385.872 1350.007 1445.483 1390.275 NA 1427.039 1430.710
[9] 1437.733 1476.392
> rowVars(tmp5)
[1] 7990.22768 86.28743 78.24580 94.84344 91.82144 46.75944
[7] 68.70438 60.47470 58.79530 65.13045
> rowSd(tmp5)
[1] 89.388073 9.289103 8.845665 9.738760 9.582351 6.838088 8.288810
[8] 7.776548 7.667810 8.070344
> rowMax(tmp5)
[1] 469.87799 86.70444 82.48503 94.10051 94.01837 NA 91.99447
[8] 83.41669 89.26876 89.40904
> rowMin(tmp5)
[1] 56.37239 52.64637 55.20141 56.59591 56.67122 NA 58.26414 53.73983
[9] 53.30397 55.29035
>
> colMeans(tmp5)
[1] 111.99303 71.35430 71.89059 71.07375 69.87386 70.55622 68.76936
[8] 71.28381 71.40024 69.58114 71.40622 75.40983 71.85651 71.39384
[15] 72.09036 67.82502 NA 70.85989 74.00388 68.47751
> colSums(tmp5)
[1] 1119.9303 713.5430 718.9059 710.7375 698.7386 705.5622 687.6936
[8] 712.8381 714.0024 695.8114 714.0622 754.0983 718.5651 713.9384
[15] 720.9036 678.2502 NA 708.5989 740.0388 684.7751
> colVars(tmp5)
[1] 15872.49108 108.27052 132.97217 48.20997 56.96864 119.47337
[7] 44.53562 71.05330 68.74984 29.56519 84.95239 33.82408
[13] 82.00065 158.18078 63.69476 30.33556 NA 87.72166
[19] 93.96111 85.72141
> colSd(tmp5)
[1] 125.986075 10.405312 11.531356 6.943340 7.547757 10.930387
[7] 6.673501 8.429312 8.291552 5.437388 9.216962 5.815848
[13] 9.055421 12.576994 7.980900 5.507772 NA 9.365984
[19] 9.693354 9.258586
> colMax(tmp5)
[1] 469.87799 86.03539 84.30554 82.80534 82.39391 91.99447 77.69016
[8] 82.48503 87.50260 78.28490 86.70444 82.86622 85.19838 94.10051
[15] 88.57629 76.01074 NA 83.75260 89.26876 85.69660
> colMin(tmp5)
[1] 60.40136 55.20141 52.64637 61.92950 60.19377 56.37239 55.29035 53.73983
[9] 57.94584 62.23904 56.21127 66.43507 61.07632 59.93252 56.67122 58.49981
[17] NA 53.30397 55.48988 56.33974
>
> Max(tmp5,na.rm=TRUE)
[1] 469.878
> Min(tmp5,na.rm=TRUE)
[1] 52.64637
> mean(tmp5,na.rm=TRUE)
[1] 73.06719
> Sum(tmp5,na.rm=TRUE)
[1] 14540.37
> Var(tmp5,na.rm=TRUE)
[1] 871.7413
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.91633 69.29361 67.50036 72.27415 69.51373 71.50177 71.35195 71.53548
[9] 71.88667 73.81962
> rowSums(tmp5,na.rm=TRUE)
[1] 1838.327 1385.872 1350.007 1445.483 1390.275 1358.534 1427.039 1430.710
[9] 1437.733 1476.392
> rowVars(tmp5,na.rm=TRUE)
[1] 7990.22768 86.28743 78.24580 94.84344 91.82144 46.75944
[7] 68.70438 60.47470 58.79530 65.13045
> rowSd(tmp5,na.rm=TRUE)
[1] 89.388073 9.289103 8.845665 9.738760 9.582351 6.838088 8.288810
[8] 7.776548 7.667810 8.070344
> rowMax(tmp5,na.rm=TRUE)
[1] 469.87799 86.70444 82.48503 94.10051 94.01837 82.80534 91.99447
[8] 83.41669 89.26876 89.40904
> rowMin(tmp5,na.rm=TRUE)
[1] 56.37239 52.64637 55.20141 56.59591 56.67122 59.93252 58.26414 53.73983
[9] 53.30397 55.29035
>
> colMeans(tmp5,na.rm=TRUE)
[1] 111.99303 71.35430 71.89059 71.07375 69.87386 70.55622 68.76936
[8] 71.28381 71.40024 69.58114 71.40622 75.40983 71.85651 71.39384
[15] 72.09036 67.82502 69.93088 70.85989 74.00388 68.47751
> colSums(tmp5,na.rm=TRUE)
[1] 1119.9303 713.5430 718.9059 710.7375 698.7386 705.5622 687.6936
[8] 712.8381 714.0024 695.8114 714.0622 754.0983 718.5651 713.9384
[15] 720.9036 678.2502 629.3779 708.5989 740.0388 684.7751
> colVars(tmp5,na.rm=TRUE)
[1] 15872.49108 108.27052 132.97217 48.20997 56.96864 119.47337
[7] 44.53562 71.05330 68.74984 29.56519 84.95239 33.82408
[13] 82.00065 158.18078 63.69476 30.33556 77.31377 87.72166
[19] 93.96111 85.72141
> colSd(tmp5,na.rm=TRUE)
[1] 125.986075 10.405312 11.531356 6.943340 7.547757 10.930387
[7] 6.673501 8.429312 8.291552 5.437388 9.216962 5.815848
[13] 9.055421 12.576994 7.980900 5.507772 8.792825 9.365984
[19] 9.693354 9.258586
> colMax(tmp5,na.rm=TRUE)
[1] 469.87799 86.03539 84.30554 82.80534 82.39391 91.99447 77.69016
[8] 82.48503 87.50260 78.28490 86.70444 82.86622 85.19838 94.10051
[15] 88.57629 76.01074 79.68899 83.75260 89.26876 85.69660
> colMin(tmp5,na.rm=TRUE)
[1] 60.40136 55.20141 52.64637 61.92950 60.19377 56.37239 55.29035 53.73983
[9] 57.94584 62.23904 56.21127 66.43507 61.07632 59.93252 56.67122 58.49981
[17] 55.86283 53.30397 55.48988 56.33974
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.91633 69.29361 67.50036 72.27415 69.51373 NaN 71.35195 71.53548
[9] 71.88667 73.81962
> rowSums(tmp5,na.rm=TRUE)
[1] 1838.327 1385.872 1350.007 1445.483 1390.275 0.000 1427.039 1430.710
[9] 1437.733 1476.392
> rowVars(tmp5,na.rm=TRUE)
[1] 7990.22768 86.28743 78.24580 94.84344 91.82144 NA
[7] 68.70438 60.47470 58.79530 65.13045
> rowSd(tmp5,na.rm=TRUE)
[1] 89.388073 9.289103 8.845665 9.738760 9.582351 NA 8.288810
[8] 7.776548 7.667810 8.070344
> rowMax(tmp5,na.rm=TRUE)
[1] 469.87799 86.70444 82.48503 94.10051 94.01837 NA 91.99447
[8] 83.41669 89.26876 89.40904
> rowMin(tmp5,na.rm=TRUE)
[1] 56.37239 52.64637 55.20141 56.59591 56.67122 NA 58.26414 53.73983
[9] 53.30397 55.29035
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 116.58504 71.27877 71.03460 69.77024 70.94943 70.74442 67.77816
[8] 71.15258 71.23833 68.82678 70.52412 74.85787 73.05431 72.66732
[15] 72.83887 67.45092 NaN 70.87474 74.84392 68.24736
> colSums(tmp5,na.rm=TRUE)
[1] 1049.2653 641.5089 639.3114 627.9321 638.5448 636.6998 610.0035
[8] 640.3732 641.1450 619.4411 634.7170 673.7208 657.4887 654.0059
[15] 655.5498 607.0583 0.0000 637.8726 673.5953 614.2262
> colVars(tmp5,na.rm=TRUE)
[1] 17619.32882 121.74016 141.35064 35.12091 51.07525 134.00907
[7] 39.04970 79.74122 77.04865 26.85898 86.81776 34.62473
[13] 76.11013 159.70867 65.35369 32.55303 NA 98.68438
[19] 97.76745 95.84068
> colSd(tmp5,na.rm=TRUE)
[1] 132.737820 11.033592 11.889098 5.926290 7.146695 11.576228
[7] 6.248976 8.929794 8.777736 5.182565 9.317605 5.884278
[13] 8.724112 12.637590 8.084163 5.705527 NA 9.934001
[19] 9.887742 9.789825
> colMax(tmp5,na.rm=TRUE)
[1] 469.87799 86.03539 84.30554 77.49933 82.39391 91.99447 77.52713
[8] 82.48503 87.50260 78.28490 86.70444 82.86622 85.19838 94.10051
[15] 88.57629 76.01074 -Inf 83.75260 89.26876 85.69660
> colMin(tmp5,na.rm=TRUE)
[1] 60.40136 55.20141 52.64637 61.92950 61.21568 56.37239 55.29035 53.73983
[9] 57.94584 62.23904 56.21127 66.43507 62.01262 60.26755 56.67122 58.49981
[17] Inf 53.30397 55.48988 56.33974
>
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 3
> which.col <- 1
> cat(which.row," ",which.col,"\n")
3 1
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> rowVars(tmp5,na.rm=TRUE)
[1] 375.55243 199.53076 135.73300 195.88422 370.26006 67.12758 275.94912
[8] 245.84397 232.57763 224.44992
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 375.55243 199.53076 135.73300 195.88422 370.26006 67.12758 275.94912
[8] 245.84397 232.57763 224.44992
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] 5.684342e-14 0.000000e+00 1.421085e-14 -1.136868e-13 -3.410605e-13
[6] -2.273737e-13 -1.136868e-13 2.842171e-13 0.000000e+00 0.000000e+00
[11] -2.842171e-14 7.105427e-14 4.263256e-14 0.000000e+00 -5.684342e-14
[16] -9.947598e-14 8.526513e-14 -1.705303e-13 -1.705303e-13 2.842171e-14
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
1 10
5 20
1 18
5 1
1 11
3 19
10 5
10 12
1 16
3 19
8 2
8 4
9 4
7 18
4 20
9 13
5 14
1 17
2 20
3 6
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> ### now test 1 by n and n by 1 matrix
>
>
> err.tol <- 1e-12
>
> rm(tmp5)
>
> dataset1 <- rnorm(100)
> dataset2 <- rnorm(100)
>
> tmp <- createBufferedMatrix(1,100)
> tmp[1,] <- dataset1
>
> tmp2 <- createBufferedMatrix(100,1)
> tmp2[,1] <- dataset2
>
>
>
>
>
> Max(tmp)
[1] 2.622881
> Min(tmp)
[1] -2.780017
> mean(tmp)
[1] -0.0267654
> Sum(tmp)
[1] -2.67654
> Var(tmp)
[1] 0.930901
>
> rowMeans(tmp)
[1] -0.0267654
> rowSums(tmp)
[1] -2.67654
> rowVars(tmp)
[1] 0.930901
> rowSd(tmp)
[1] 0.9648321
> rowMax(tmp)
[1] 2.622881
> rowMin(tmp)
[1] -2.780017
>
> colMeans(tmp)
[1] -0.548871143 -0.779396055 -0.881204426 -0.357056296 -0.260285926
[6] 1.609900228 0.122938944 -0.261080099 -0.185537146 0.833390618
[11] -1.515910448 0.206481600 -0.810884493 -0.617006682 0.551946622
[16] 0.292079935 -0.492698282 1.053213154 -0.178095264 -1.253964309
[21] -0.251876349 -0.230192077 1.633363626 2.145383864 -0.040270806
[26] 1.009053069 -2.780017065 -0.628799354 1.206073264 0.496546836
[31] 0.509012641 -0.975682926 -0.102527809 1.200485259 -1.676469235
[36] -1.179370350 0.393512980 -1.060718861 -1.180644894 0.129227066
[41] 0.447348914 -0.270917768 -0.263211525 -1.686536643 0.223140889
[46] -0.532100115 -0.268073798 -0.470730025 0.005929051 -1.122196248
[51] 0.892907913 0.229892974 -0.237059934 1.368898062 -0.130118605
[56] 0.166937720 -0.502672212 -0.200493675 -0.532987910 0.266991837
[61] 0.685200874 -0.070336634 0.232264047 0.896792897 -0.759348611
[66] -0.387804344 -0.336181545 -1.381188067 2.622880957 -0.652747049
[71] -1.908395720 0.378178117 1.295907059 -0.560992255 -0.014821980
[76] -2.216818271 1.056457626 1.708015693 0.762546657 0.928819951
[81] -0.474940917 0.910116879 0.447009528 0.358454732 0.907340102
[86] -0.349092633 0.891133367 -1.052719155 0.581698448 -0.984595828
[91] 0.759505567 -0.807030298 1.271219276 0.583200176 -1.330858807
[96] 0.707256197 -1.580937486 0.081767138 -0.083366703 1.680872550
> colSums(tmp)
[1] -0.548871143 -0.779396055 -0.881204426 -0.357056296 -0.260285926
[6] 1.609900228 0.122938944 -0.261080099 -0.185537146 0.833390618
[11] -1.515910448 0.206481600 -0.810884493 -0.617006682 0.551946622
[16] 0.292079935 -0.492698282 1.053213154 -0.178095264 -1.253964309
[21] -0.251876349 -0.230192077 1.633363626 2.145383864 -0.040270806
[26] 1.009053069 -2.780017065 -0.628799354 1.206073264 0.496546836
[31] 0.509012641 -0.975682926 -0.102527809 1.200485259 -1.676469235
[36] -1.179370350 0.393512980 -1.060718861 -1.180644894 0.129227066
[41] 0.447348914 -0.270917768 -0.263211525 -1.686536643 0.223140889
[46] -0.532100115 -0.268073798 -0.470730025 0.005929051 -1.122196248
[51] 0.892907913 0.229892974 -0.237059934 1.368898062 -0.130118605
[56] 0.166937720 -0.502672212 -0.200493675 -0.532987910 0.266991837
[61] 0.685200874 -0.070336634 0.232264047 0.896792897 -0.759348611
[66] -0.387804344 -0.336181545 -1.381188067 2.622880957 -0.652747049
[71] -1.908395720 0.378178117 1.295907059 -0.560992255 -0.014821980
[76] -2.216818271 1.056457626 1.708015693 0.762546657 0.928819951
[81] -0.474940917 0.910116879 0.447009528 0.358454732 0.907340102
[86] -0.349092633 0.891133367 -1.052719155 0.581698448 -0.984595828
[91] 0.759505567 -0.807030298 1.271219276 0.583200176 -1.330858807
[96] 0.707256197 -1.580937486 0.081767138 -0.083366703 1.680872550
> colVars(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colSd(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colMax(tmp)
[1] -0.548871143 -0.779396055 -0.881204426 -0.357056296 -0.260285926
[6] 1.609900228 0.122938944 -0.261080099 -0.185537146 0.833390618
[11] -1.515910448 0.206481600 -0.810884493 -0.617006682 0.551946622
[16] 0.292079935 -0.492698282 1.053213154 -0.178095264 -1.253964309
[21] -0.251876349 -0.230192077 1.633363626 2.145383864 -0.040270806
[26] 1.009053069 -2.780017065 -0.628799354 1.206073264 0.496546836
[31] 0.509012641 -0.975682926 -0.102527809 1.200485259 -1.676469235
[36] -1.179370350 0.393512980 -1.060718861 -1.180644894 0.129227066
[41] 0.447348914 -0.270917768 -0.263211525 -1.686536643 0.223140889
[46] -0.532100115 -0.268073798 -0.470730025 0.005929051 -1.122196248
[51] 0.892907913 0.229892974 -0.237059934 1.368898062 -0.130118605
[56] 0.166937720 -0.502672212 -0.200493675 -0.532987910 0.266991837
[61] 0.685200874 -0.070336634 0.232264047 0.896792897 -0.759348611
[66] -0.387804344 -0.336181545 -1.381188067 2.622880957 -0.652747049
[71] -1.908395720 0.378178117 1.295907059 -0.560992255 -0.014821980
[76] -2.216818271 1.056457626 1.708015693 0.762546657 0.928819951
[81] -0.474940917 0.910116879 0.447009528 0.358454732 0.907340102
[86] -0.349092633 0.891133367 -1.052719155 0.581698448 -0.984595828
[91] 0.759505567 -0.807030298 1.271219276 0.583200176 -1.330858807
[96] 0.707256197 -1.580937486 0.081767138 -0.083366703 1.680872550
> colMin(tmp)
[1] -0.548871143 -0.779396055 -0.881204426 -0.357056296 -0.260285926
[6] 1.609900228 0.122938944 -0.261080099 -0.185537146 0.833390618
[11] -1.515910448 0.206481600 -0.810884493 -0.617006682 0.551946622
[16] 0.292079935 -0.492698282 1.053213154 -0.178095264 -1.253964309
[21] -0.251876349 -0.230192077 1.633363626 2.145383864 -0.040270806
[26] 1.009053069 -2.780017065 -0.628799354 1.206073264 0.496546836
[31] 0.509012641 -0.975682926 -0.102527809 1.200485259 -1.676469235
[36] -1.179370350 0.393512980 -1.060718861 -1.180644894 0.129227066
[41] 0.447348914 -0.270917768 -0.263211525 -1.686536643 0.223140889
[46] -0.532100115 -0.268073798 -0.470730025 0.005929051 -1.122196248
[51] 0.892907913 0.229892974 -0.237059934 1.368898062 -0.130118605
[56] 0.166937720 -0.502672212 -0.200493675 -0.532987910 0.266991837
[61] 0.685200874 -0.070336634 0.232264047 0.896792897 -0.759348611
[66] -0.387804344 -0.336181545 -1.381188067 2.622880957 -0.652747049
[71] -1.908395720 0.378178117 1.295907059 -0.560992255 -0.014821980
[76] -2.216818271 1.056457626 1.708015693 0.762546657 0.928819951
[81] -0.474940917 0.910116879 0.447009528 0.358454732 0.907340102
[86] -0.349092633 0.891133367 -1.052719155 0.581698448 -0.984595828
[91] 0.759505567 -0.807030298 1.271219276 0.583200176 -1.330858807
[96] 0.707256197 -1.580937486 0.081767138 -0.083366703 1.680872550
> colMedians(tmp)
[1] -0.548871143 -0.779396055 -0.881204426 -0.357056296 -0.260285926
[6] 1.609900228 0.122938944 -0.261080099 -0.185537146 0.833390618
[11] -1.515910448 0.206481600 -0.810884493 -0.617006682 0.551946622
[16] 0.292079935 -0.492698282 1.053213154 -0.178095264 -1.253964309
[21] -0.251876349 -0.230192077 1.633363626 2.145383864 -0.040270806
[26] 1.009053069 -2.780017065 -0.628799354 1.206073264 0.496546836
[31] 0.509012641 -0.975682926 -0.102527809 1.200485259 -1.676469235
[36] -1.179370350 0.393512980 -1.060718861 -1.180644894 0.129227066
[41] 0.447348914 -0.270917768 -0.263211525 -1.686536643 0.223140889
[46] -0.532100115 -0.268073798 -0.470730025 0.005929051 -1.122196248
[51] 0.892907913 0.229892974 -0.237059934 1.368898062 -0.130118605
[56] 0.166937720 -0.502672212 -0.200493675 -0.532987910 0.266991837
[61] 0.685200874 -0.070336634 0.232264047 0.896792897 -0.759348611
[66] -0.387804344 -0.336181545 -1.381188067 2.622880957 -0.652747049
[71] -1.908395720 0.378178117 1.295907059 -0.560992255 -0.014821980
[76] -2.216818271 1.056457626 1.708015693 0.762546657 0.928819951
[81] -0.474940917 0.910116879 0.447009528 0.358454732 0.907340102
[86] -0.349092633 0.891133367 -1.052719155 0.581698448 -0.984595828
[91] 0.759505567 -0.807030298 1.271219276 0.583200176 -1.330858807
[96] 0.707256197 -1.580937486 0.081767138 -0.083366703 1.680872550
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.5488711 -0.7793961 -0.8812044 -0.3570563 -0.2602859 1.6099 0.1229389
[2,] -0.5488711 -0.7793961 -0.8812044 -0.3570563 -0.2602859 1.6099 0.1229389
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -0.2610801 -0.1855371 0.8333906 -1.51591 0.2064816 -0.8108845 -0.6170067
[2,] -0.2610801 -0.1855371 0.8333906 -1.51591 0.2064816 -0.8108845 -0.6170067
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 0.5519466 0.2920799 -0.4926983 1.053213 -0.1780953 -1.253964 -0.2518763
[2,] 0.5519466 0.2920799 -0.4926983 1.053213 -0.1780953 -1.253964 -0.2518763
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -0.2301921 1.633364 2.145384 -0.04027081 1.009053 -2.780017 -0.6287994
[2,] -0.2301921 1.633364 2.145384 -0.04027081 1.009053 -2.780017 -0.6287994
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 1.206073 0.4965468 0.5090126 -0.9756829 -0.1025278 1.200485 -1.676469
[2,] 1.206073 0.4965468 0.5090126 -0.9756829 -0.1025278 1.200485 -1.676469
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -1.17937 0.393513 -1.060719 -1.180645 0.1292271 0.4473489 -0.2709178
[2,] -1.17937 0.393513 -1.060719 -1.180645 0.1292271 0.4473489 -0.2709178
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.2632115 -1.686537 0.2231409 -0.5321001 -0.2680738 -0.47073 0.005929051
[2,] -0.2632115 -1.686537 0.2231409 -0.5321001 -0.2680738 -0.47073 0.005929051
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -1.122196 0.8929079 0.229893 -0.2370599 1.368898 -0.1301186 0.1669377
[2,] -1.122196 0.8929079 0.229893 -0.2370599 1.368898 -0.1301186 0.1669377
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -0.5026722 -0.2004937 -0.5329879 0.2669918 0.6852009 -0.07033663 0.232264
[2,] -0.5026722 -0.2004937 -0.5329879 0.2669918 0.6852009 -0.07033663 0.232264
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.8967929 -0.7593486 -0.3878043 -0.3361815 -1.381188 2.622881 -0.652747
[2,] 0.8967929 -0.7593486 -0.3878043 -0.3361815 -1.381188 2.622881 -0.652747
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -1.908396 0.3781781 1.295907 -0.5609923 -0.01482198 -2.216818 1.056458
[2,] -1.908396 0.3781781 1.295907 -0.5609923 -0.01482198 -2.216818 1.056458
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 1.708016 0.7625467 0.92882 -0.4749409 0.9101169 0.4470095 0.3584547
[2,] 1.708016 0.7625467 0.92882 -0.4749409 0.9101169 0.4470095 0.3584547
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] 0.9073401 -0.3490926 0.8911334 -1.052719 0.5816984 -0.9845958 0.7595056
[2,] 0.9073401 -0.3490926 0.8911334 -1.052719 0.5816984 -0.9845958 0.7595056
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -0.8070303 1.271219 0.5832002 -1.330859 0.7072562 -1.580937 0.08176714
[2,] -0.8070303 1.271219 0.5832002 -1.330859 0.7072562 -1.580937 0.08176714
[,99] [,100]
[1,] -0.0833667 1.680873
[2,] -0.0833667 1.680873
>
>
> Max(tmp2)
[1] 2.068509
> Min(tmp2)
[1] -2.401027
> mean(tmp2)
[1] 0.01827467
> Sum(tmp2)
[1] 1.827467
> Var(tmp2)
[1] 0.9649516
>
> rowMeans(tmp2)
[1] -0.90149151 -1.19970415 -0.14328903 0.73341909 0.10901862 0.85449501
[7] -1.77632872 0.06256149 0.54641936 -0.02476825 0.64983738 -0.33399585
[13] 0.96985858 1.11078508 0.11627555 -0.22591917 -0.08603804 2.02361681
[19] -1.27314472 1.28383973 0.29384659 0.62769978 -1.12679297 1.24586921
[25] -1.38803024 -1.36367996 -1.77939198 -0.47233573 0.19803268 -0.29181226
[31] 0.61980269 -0.88677999 0.28826698 -0.77223821 1.26350947 2.06850851
[37] -1.02543392 -0.85063226 -0.79583905 -0.42396999 -0.32260349 0.75154988
[43] 1.30849223 -0.61969150 0.16696242 1.22975959 0.80567905 1.89075807
[49] -0.14699142 1.18182081 1.48544217 0.86152138 -0.19582044 1.18539479
[55] 1.19299309 1.82359459 -0.53688660 -1.21436558 -0.12620937 -0.61474204
[61] 0.63756093 -2.40102653 0.36581841 0.62229775 0.44831453 -2.05589986
[67] 0.80650721 -0.88149061 -0.03896171 -0.16955046 -0.76430119 0.48443313
[73] -0.61643748 -0.51402807 0.06673144 -0.47483818 -0.31499017 0.39181906
[79] -0.68513058 0.58635989 -1.90806571 -0.62756919 -0.35607558 -0.75012638
[85] -0.66065412 -1.24132217 0.56567057 1.39875501 0.25774825 0.63318993
[91] -1.83720750 -0.17101885 0.04724139 -0.44196615 0.14419153 1.01273945
[97] 1.75594833 1.63028198 -1.03031565 -0.11786980
> rowSums(tmp2)
[1] -0.90149151 -1.19970415 -0.14328903 0.73341909 0.10901862 0.85449501
[7] -1.77632872 0.06256149 0.54641936 -0.02476825 0.64983738 -0.33399585
[13] 0.96985858 1.11078508 0.11627555 -0.22591917 -0.08603804 2.02361681
[19] -1.27314472 1.28383973 0.29384659 0.62769978 -1.12679297 1.24586921
[25] -1.38803024 -1.36367996 -1.77939198 -0.47233573 0.19803268 -0.29181226
[31] 0.61980269 -0.88677999 0.28826698 -0.77223821 1.26350947 2.06850851
[37] -1.02543392 -0.85063226 -0.79583905 -0.42396999 -0.32260349 0.75154988
[43] 1.30849223 -0.61969150 0.16696242 1.22975959 0.80567905 1.89075807
[49] -0.14699142 1.18182081 1.48544217 0.86152138 -0.19582044 1.18539479
[55] 1.19299309 1.82359459 -0.53688660 -1.21436558 -0.12620937 -0.61474204
[61] 0.63756093 -2.40102653 0.36581841 0.62229775 0.44831453 -2.05589986
[67] 0.80650721 -0.88149061 -0.03896171 -0.16955046 -0.76430119 0.48443313
[73] -0.61643748 -0.51402807 0.06673144 -0.47483818 -0.31499017 0.39181906
[79] -0.68513058 0.58635989 -1.90806571 -0.62756919 -0.35607558 -0.75012638
[85] -0.66065412 -1.24132217 0.56567057 1.39875501 0.25774825 0.63318993
[91] -1.83720750 -0.17101885 0.04724139 -0.44196615 0.14419153 1.01273945
[97] 1.75594833 1.63028198 -1.03031565 -0.11786980
> rowVars(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowSd(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowMax(tmp2)
[1] -0.90149151 -1.19970415 -0.14328903 0.73341909 0.10901862 0.85449501
[7] -1.77632872 0.06256149 0.54641936 -0.02476825 0.64983738 -0.33399585
[13] 0.96985858 1.11078508 0.11627555 -0.22591917 -0.08603804 2.02361681
[19] -1.27314472 1.28383973 0.29384659 0.62769978 -1.12679297 1.24586921
[25] -1.38803024 -1.36367996 -1.77939198 -0.47233573 0.19803268 -0.29181226
[31] 0.61980269 -0.88677999 0.28826698 -0.77223821 1.26350947 2.06850851
[37] -1.02543392 -0.85063226 -0.79583905 -0.42396999 -0.32260349 0.75154988
[43] 1.30849223 -0.61969150 0.16696242 1.22975959 0.80567905 1.89075807
[49] -0.14699142 1.18182081 1.48544217 0.86152138 -0.19582044 1.18539479
[55] 1.19299309 1.82359459 -0.53688660 -1.21436558 -0.12620937 -0.61474204
[61] 0.63756093 -2.40102653 0.36581841 0.62229775 0.44831453 -2.05589986
[67] 0.80650721 -0.88149061 -0.03896171 -0.16955046 -0.76430119 0.48443313
[73] -0.61643748 -0.51402807 0.06673144 -0.47483818 -0.31499017 0.39181906
[79] -0.68513058 0.58635989 -1.90806571 -0.62756919 -0.35607558 -0.75012638
[85] -0.66065412 -1.24132217 0.56567057 1.39875501 0.25774825 0.63318993
[91] -1.83720750 -0.17101885 0.04724139 -0.44196615 0.14419153 1.01273945
[97] 1.75594833 1.63028198 -1.03031565 -0.11786980
> rowMin(tmp2)
[1] -0.90149151 -1.19970415 -0.14328903 0.73341909 0.10901862 0.85449501
[7] -1.77632872 0.06256149 0.54641936 -0.02476825 0.64983738 -0.33399585
[13] 0.96985858 1.11078508 0.11627555 -0.22591917 -0.08603804 2.02361681
[19] -1.27314472 1.28383973 0.29384659 0.62769978 -1.12679297 1.24586921
[25] -1.38803024 -1.36367996 -1.77939198 -0.47233573 0.19803268 -0.29181226
[31] 0.61980269 -0.88677999 0.28826698 -0.77223821 1.26350947 2.06850851
[37] -1.02543392 -0.85063226 -0.79583905 -0.42396999 -0.32260349 0.75154988
[43] 1.30849223 -0.61969150 0.16696242 1.22975959 0.80567905 1.89075807
[49] -0.14699142 1.18182081 1.48544217 0.86152138 -0.19582044 1.18539479
[55] 1.19299309 1.82359459 -0.53688660 -1.21436558 -0.12620937 -0.61474204
[61] 0.63756093 -2.40102653 0.36581841 0.62229775 0.44831453 -2.05589986
[67] 0.80650721 -0.88149061 -0.03896171 -0.16955046 -0.76430119 0.48443313
[73] -0.61643748 -0.51402807 0.06673144 -0.47483818 -0.31499017 0.39181906
[79] -0.68513058 0.58635989 -1.90806571 -0.62756919 -0.35607558 -0.75012638
[85] -0.66065412 -1.24132217 0.56567057 1.39875501 0.25774825 0.63318993
[91] -1.83720750 -0.17101885 0.04724139 -0.44196615 0.14419153 1.01273945
[97] 1.75594833 1.63028198 -1.03031565 -0.11786980
>
> colMeans(tmp2)
[1] 0.01827467
> colSums(tmp2)
[1] 1.827467
> colVars(tmp2)
[1] 0.9649516
> colSd(tmp2)
[1] 0.9823195
> colMax(tmp2)
[1] 2.068509
> colMin(tmp2)
[1] -2.401027
> colMedians(tmp2)
[1] -0.03186498
> colRanges(tmp2)
[,1]
[1,] -2.401027
[2,] 2.068509
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] -1.1493347 5.1070076 3.3619668 4.3280851 4.8581018 6.8529392
[7] -1.8152296 0.1964481 -1.1043268 3.6830271
> colApply(tmp,quantile)[,1]
[,1]
[1,] -2.25063443
[2,] -0.38532303
[3,] -0.08633593
[4,] 0.22275256
[5,] 1.67584075
>
> rowApply(tmp,sum)
[1] 1.6101509 4.2176625 8.4500886 -1.3072008 -3.3362753 3.5187536
[7] 9.5982710 3.9418297 -2.7255851 0.3509895
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 4 6 7 5 4 4 2 1 1 10
[2,] 5 9 2 8 5 1 8 4 9 5
[3,] 1 1 4 7 10 3 9 9 4 9
[4,] 6 4 3 6 9 10 6 10 3 2
[5,] 10 3 6 2 3 9 10 8 8 8
[6,] 8 7 9 10 6 7 7 7 7 3
[7,] 2 2 5 4 7 2 3 2 5 6
[8,] 3 5 8 9 2 8 4 3 2 4
[9,] 9 8 10 1 1 5 1 6 6 1
[10,] 7 10 1 3 8 6 5 5 10 7
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -3.1629531 -0.9851526 -1.2915008 2.2067514 1.5589988 1.8324459
[7] 0.6595905 -2.9740395 3.8220412 0.1243613 -0.8420506 1.8175641
[13] -0.8555770 -2.1852828 -2.1468239 -1.0056261 -1.7192500 0.6023358
[19] -2.1510304 1.2455363
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.22534240
[2,] -1.10640370
[3,] -0.42449274
[4,] -0.33968243
[5,] -0.06703187
>
> rowApply(tmp,sum)
[1] 1.391325 -4.933877 3.290448 1.345488 -6.543046
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 7 9 3 7 4
[2,] 5 10 14 19 1
[3,] 20 2 2 10 14
[4,] 8 18 19 15 9
[5,] 13 7 20 16 13
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.33968243 -0.3961879 1.4454530 -0.3119538 -0.01563895 1.2320525
[2,] -0.42449274 -0.4077086 -1.7799556 1.1119192 -0.72574794 0.5203555
[3,] -1.22534240 0.7561432 -1.3666312 1.4384878 1.52600125 1.1541286
[4,] -0.06703187 1.1299422 0.2565139 0.6263527 0.75315394 -0.2947499
[5,] -1.10640370 -2.0673415 0.1531191 -0.6580545 0.02123045 -0.7793409
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 0.2026354 -0.64008919 -0.2392063 -0.5818344 -0.1870279 0.4766302
[2,] 0.8368535 0.08810269 1.4083551 1.8087417 -1.7794334 -0.1658817
[3,] 0.7306944 -0.75456147 1.1767582 -0.8266203 0.6866074 0.6203954
[4,] -0.1110372 -0.71140655 1.0257599 0.3185933 -0.8192149 0.1592034
[5,] -0.9995556 -0.95608500 0.4503743 -0.5945190 1.2570182 0.7272168
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -0.2268808 0.7840937 0.92385937 1.1259918 -0.56914963 -0.3783027
[2,] -2.2299874 -0.9067134 0.31340193 -0.4541742 -0.97220442 -0.2381071
[3,] 0.9117014 0.1430078 -0.01897977 -0.4136162 -0.21900383 -0.4918094
[4,] 0.3284917 -1.7484982 -2.58950237 0.4286995 0.12701836 0.9044837
[5,] 0.3610981 -0.4571727 -0.77560310 -1.6925271 -0.08591046 0.8060713
[,19] [,20]
[1,] -0.74322307 -0.1702143
[2,] -0.03396606 -0.9032337
[3,] -1.39832996 0.8614175
[4,] 1.17487953 0.4538366
[5,] -1.15039085 1.0037302
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 648 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 563 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 480 bytes.
>
>
> rm(tmp)
>
>
> ###
> ### Testing colnames and rownames
> ###
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
>
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7
row1 0.803015 -0.4417372 -0.732723 -0.464035 -1.950328 -0.9012985 1.081257
col8 col9 col10 col11 col12 col13 col14
row1 -0.02212121 -0.2713689 -0.1971587 -0.4636746 -0.576657 0.3669206 -1.086286
col15 col16 col17 col18 col19 col20
row1 -0.1053536 0.8227868 -1.034301 0.1663382 -0.007234198 0.7938816
> tmp[,"col10"]
col10
row1 -0.19715870
row2 -1.68521737
row3 -1.33786806
row4 -0.03285052
row5 -0.29605088
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 0.8030150 -0.4417372 -0.73272304 -0.4640350 -1.950328 -0.9012985 1.081257
row5 0.7407448 1.4734507 -0.06701714 0.4385033 1.605629 -0.4165061 -1.090562
col8 col9 col10 col11 col12 col13
row1 -0.02212121 -0.2713689 -0.1971587 -0.4636746 -0.576657 0.3669206
row5 0.68225767 1.0351456 -0.2960509 -0.7363085 3.281356 -0.2319642
col14 col15 col16 col17 col18 col19
row1 -1.0862858 -0.1053536 0.8227868 -1.034301 0.16633817 -0.007234198
row5 -0.1953449 0.9678066 -0.6871076 -3.031140 -0.04399016 0.201734690
col20
row1 0.79388158
row5 -0.08397402
> tmp[,c("col6","col20")]
col6 col20
row1 -0.90129848 0.79388158
row2 -0.06985275 -1.76014121
row3 -0.20750472 0.10024261
row4 -0.99059917 -2.14946259
row5 -0.41650609 -0.08397402
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -0.9012985 0.79388158
row5 -0.4165061 -0.08397402
>
>
>
>
> tmp["row1",] <- rnorm(20,mean=10)
> tmp[,"col10"] <- rnorm(5,mean=30)
> tmp[c("row1","row5"),] <- rnorm(40,mean=50)
> tmp[,c("col6","col20")] <- rnorm(10,mean=75)
> tmp[c("row1","row5"),c("col6","col20")] <- rnorm(4,mean=105)
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.63263 49.86786 50.4952 49.3427 50.07047 104.3587 51.82431 49.91202
col9 col10 col11 col12 col13 col14 col15 col16
row1 48.82768 51.38066 49.34191 50.27981 50.17496 49.73391 47.96363 50.41569
col17 col18 col19 col20
row1 50.75586 51.16133 50.5374 105.9799
> tmp[,"col10"]
col10
row1 51.38066
row2 29.83132
row3 29.08565
row4 30.08210
row5 49.26823
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.63263 49.86786 50.49520 49.34270 50.07047 104.3587 51.82431 49.91202
row5 49.23625 49.64469 50.95268 49.18815 49.43934 104.5147 49.30911 49.31945
col9 col10 col11 col12 col13 col14 col15 col16
row1 48.82768 51.38066 49.34191 50.27981 50.17496 49.73391 47.96363 50.41569
row5 50.19853 49.26823 51.34348 49.87484 49.84989 49.36810 49.38485 48.01710
col17 col18 col19 col20
row1 50.75586 51.16133 50.53740 105.9799
row5 50.36751 49.88047 49.80072 106.0728
> tmp[,c("col6","col20")]
col6 col20
row1 104.35868 105.97993
row2 73.84573 74.68928
row3 75.33204 74.85394
row4 75.35092 75.76123
row5 104.51474 106.07285
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 104.3587 105.9799
row5 104.5147 106.0728
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 104.3587 105.9799
row5 104.5147 106.0728
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -1.23231990
[2,] 0.05632458
[3,] -1.10532207
[4,] 0.27886135
[5,] 0.27128738
> tmp[,c("col17","col7")]
col17 col7
[1,] 0.03257489 0.5898454
[2,] 1.40113499 0.3154270
[3,] 0.91655768 0.2819438
[4,] -0.21854059 0.7646035
[5,] 0.67661812 -1.2888732
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 0.6035736 0.23646204
[2,] 0.4043519 -0.02697049
[3,] 0.7462487 1.37157853
[4,] 1.1596524 -1.50755510
[5,] 0.9010300 0.09648618
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 0.6035736
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 0.6035736
[2,] 0.4043519
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6]
row3 -0.6006509 -0.7123556 1.7574144 -0.2132517 0.01780431 -1.2288693
row1 -0.5219673 -0.5682005 -0.4076561 -2.3237217 -0.98258938 -0.4220166
[,7] [,8] [,9] [,10] [,11] [,12]
row3 -0.6563237 -0.6378521 -0.6498429 -0.6423272 -0.919889 -1.1896841
row1 -0.1158996 0.5924222 -0.7765053 0.8195185 -2.091056 0.8948732
[,13] [,14] [,15] [,16] [,17] [,18]
row3 -0.004118162 0.05817728 -0.8759062 1.406205 0.2589924 0.1074654
row1 -2.059909052 0.44367461 0.5908597 -2.166608 0.1772685 1.2645409
[,19] [,20]
row3 0.7567627 0.2752273
row1 -0.4012015 0.9805231
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -0.9971149 0.1961313 1.255169 -0.5493327 0.1095192 2.173281 -0.6435323
[,8] [,9] [,10]
row2 0.7256051 1.297278 -0.8640989
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.9712052 0.5500082 0.6121042 -0.2900504 0.08056003 -0.5838567 1.30299
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 0.1105103 3.691894 0.02007035 0.308764 -0.08244704 -1.11837 0.8355733
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.1141183 -1.171221 -0.435213 -1.139484 0.3966706 -0.5488514
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> colnames(tmp) <- NULL
> rownames(tmp) <- NULL
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
> dimnames(tmp) <- NULL
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
> dimnames(tmp) <- NULL
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
NULL
>
> dimnames(tmp) <- list(NULL,c(colnames(tmp,do.NULL=FALSE)))
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
>
> ###
> ### Testing logical indexing
> ###
> ###
>
> tmp <- createBufferedMatrix(230,15)
> tmp[1:230,1:15] <- rnorm(230*15)
> x <-tmp[1:230,1:15]
>
> for (rep in 1:10){
+ which.cols <- sample(c(TRUE,FALSE),15,replace=T)
+ which.rows <- sample(c(TRUE,FALSE),230,replace=T)
+
+ if (!all(tmp[which.rows,which.cols] == x[which.rows,which.cols])){
+ stop("No agreement when logical indexing\n")
+ }
+
+ if (!all(subBufferedMatrix(tmp,,which.cols)[,1:sum(which.cols)] == x[,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix cols\n")
+ }
+ if (!all(subBufferedMatrix(tmp,which.rows,)[1:sum(which.rows),] == x[which.rows,])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows\n")
+ }
+
+
+ if (!all(subBufferedMatrix(tmp,which.rows,which.cols)[1:sum(which.rows),1:sum(which.cols)]== x[which.rows,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows and columns\n")
+ }
+ }
>
>
> ##
> ## Test the ReadOnlyMode
> ##
>
> ReadOnlyMode(tmp)
<pointer: 0x60000301c120>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM70593053f0e3"
[2] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM705956ebdfde"
[3] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM705917b69467"
[4] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM705953c9025a"
[5] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM705931b98daf"
[6] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM7059d04f5aa"
[7] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM7059409c7293"
[8] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM70595f263208"
[9] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM7059449edc05"
[10] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM7059197eef75"
[11] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM70595c9af766"
[12] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM705941e87909"
[13] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM70595625fad"
[14] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM70597d77599d"
[15] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM7059269c92c5"
>
>
> ### testing coercion functions
> ###
>
> tmp <- as(tmp,"matrix")
> tmp <- as(tmp,"BufferedMatrix")
>
>
>
> ### testing whether can move storage from one location to another
>
> MoveStorageDirectory(tmp,"NewDirectory",full.path=FALSE)
<pointer: 0x600003020360>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x600003020360>
Warning message:
In dir.create(new.directory) :
'/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x600003020360>
> rowMedians(tmp)
[1] -0.295400353 0.250494485 0.515390345 0.380684903 -0.321488912
[6] 0.065585913 -0.195853194 -0.619733570 0.189477230 0.352207936
[11] 0.028168883 -0.364871767 -0.224015382 0.772994707 0.562523000
[16] -0.369654545 -0.329403381 0.019955602 0.728924050 -0.388948872
[21] 0.271468579 0.354682028 0.451617677 -0.138204624 -0.121162866
[26] -0.769795904 0.342303462 0.242847264 -0.330931611 0.088688660
[31] 0.099878203 -0.117921568 -0.537042616 0.013532496 -0.311347419
[36] 0.007094728 0.385361903 -0.068041383 -0.379027866 0.003021918
[41] 0.048300071 -0.517564019 -0.426587579 0.017533313 -0.081255765
[46] 0.150031830 -0.250189716 0.036308529 0.214912770 0.013830648
[51] -0.297627039 0.369893712 0.281354298 -0.236638735 -0.131732304
[56] 0.022863521 0.498452152 0.208706934 -0.104460855 -0.193697861
[61] -0.354518086 0.078763278 0.072155463 0.188784366 -0.040767389
[66] 0.115305907 0.002657437 0.069242159 0.344722607 -0.142340401
[71] -0.184986235 0.057857103 -0.369533093 -0.095529798 -0.133753899
[76] -0.022315742 0.406900211 -0.005903938 -0.155776015 0.044448795
[81] 0.103988453 -0.145188819 0.467607241 0.726877605 -0.153353127
[86] 0.564681513 -0.087102510 0.352129966 -0.317091958 -0.149452663
[91] 0.236437975 -0.037115872 0.099299652 0.342636296 0.491360329
[96] -0.075221128 -0.405333064 -0.037689152 0.102256990 -0.143043561
[101] 0.031218669 -0.512486636 0.240143008 0.016625967 0.326562629
[106] 0.053614107 0.597307043 0.258510862 -0.133934711 -0.071706729
[111] 0.404824110 -0.051967550 0.206146817 0.065974890 -0.778225190
[116] -0.107457739 0.290224584 0.162103973 -0.055837319 0.201106339
[121] 0.795068525 -0.110458353 0.759657635 0.171564289 0.092391288
[126] 0.554626821 0.035254435 -0.130453648 0.690839834 -0.437922446
[131] -0.058686079 0.337863759 0.205581700 0.715732655 -0.482382355
[136] -0.427243161 0.220410931 0.135520774 -0.126171676 -0.184597489
[141] -0.725530200 0.120320475 -0.070867341 -0.173691068 -0.024110723
[146] -0.315676160 -0.064059358 0.094990999 -0.357056449 0.289242392
[151] -0.082895431 -0.018603542 -0.518844781 -0.580341117 -0.059826967
[156] -0.158734276 0.092060859 0.525880785 0.655042016 0.002163579
[161] 0.113175855 0.289455793 -0.001460387 0.169515019 0.374693747
[166] 0.482228192 0.144170966 0.689337938 0.220779548 -0.041277058
[171] -0.782517627 -0.765498879 -0.469908698 0.177564737 0.051970175
[176] 0.518508455 -0.054557271 0.136247092 -0.188149956 0.752256272
[181] 0.318041804 0.035860247 -0.048592527 0.479273346 0.368307275
[186] -0.284796616 -0.439215427 -0.511440682 0.347669618 -0.404357792
[191] 0.138339510 -0.165621570 -0.287727718 0.210926595 0.030858631
[196] 0.373811470 -0.139332060 0.100011968 -0.469490349 0.224987618
[201] 0.519455068 -0.140577340 0.689147204 0.010777615 0.381570252
[206] 0.341402118 0.231818198 -0.505530084 0.366670198 -0.652584036
[211] -0.044144270 -0.381494804 0.536629061 0.355721853 -0.292971667
[216] -0.240725813 0.094970650 0.189011137 0.235542538 0.927720612
[221] -0.395183801 -0.487172535 0.399953618 -0.515941317 -0.042222339
[226] 0.238773792 -0.009619835 -0.025145063 1.006271693 -0.110979759
>
> proc.time()
user system elapsed
2.194 9.751 18.837
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> prefix <- "dbmtest"
> directory <- getwd()
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x6000037b0300>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x6000037b0300>
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x6000037b0300>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000 0.000000 0.000000 0.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000 0.000000 0.000000 0.000000 0.000000
<pointer: 0x6000037b0300>
> rm(P)
>
> #P <- .Call("R_bm_Destroy",P)
> #.Call("R_bm_Destroy",P)
> #.Call("R_bm_Test_C",P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 0
Buffer Rows: 1
Buffer Cols: 1
Printing Values
<pointer: 0x6000037b81e0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000037b81e0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 1
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000
0.000000
0.000000
0.000000
0.000000
<pointer: 0x6000037b81e0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000037b81e0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x6000037b81e0>
> rm(P)
>
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000037b8360>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000037b8360>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x6000037b8360>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x6000037b8360>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x6000037b8360>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x6000037b8360>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x6000037b8360>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x6000037b8360>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x6000037b8360>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000037bc240>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x6000037bc240>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000037bc240>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000037bc240>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile78c926bcda0a" "BufferedMatrixFile78c9388eda64"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile78c926bcda0a" "BufferedMatrixFile78c9388eda64"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000037bc480>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000037bc480>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x6000037bc480>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x6000037bc480>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x6000037bc480>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x6000037bc480>
> .Call("R_bm_isRowMode",P)
[1] FALSE
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000037bc660>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000037bc660>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x6000037bc660>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x6000037bc660>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x6000037bc840>
> .Call("R_bm_getValue",P,3,3)
[1] 6
>
> .Call("R_bm_getValue",P,100000,10000)
[1] NA
> .Call("R_bm_setValue",P,3,3,12345.0)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 12345.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x6000037bc840>
> rm(P)
>
> proc.time()
user system elapsed
0.354 0.110 0.561
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> Temp <- createBufferedMatrix(100)
> dim(Temp)
[1] 100 0
> buffer.dim(Temp)
[1] 1 1
>
>
> proc.time()
user system elapsed
0.339 0.076 0.547