Ben Bolstad
| Snapshot Date: 2025-10-23 14:17 -0400 (Thu, 23 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: devel |
| git_last_commit: 0147962 |
| git_last_commit_date: 2025-04-15 09:39:39 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-24 12:04 -0400 (Fri, 24 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 257/2359 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.73.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 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: 1.73.0 |
| 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_1.73.0.tar.gz |
| StartedAt: 2025-10-23 19:49:31 -0400 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-23 19:50:18 -0400 (Thu, 23 Oct 2025) |
| EllapsedTime: 47.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### 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_1.73.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.73.0’
* 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 14.0.0 (clang-1400.0.29.202)’
* 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-x86_64/Resources/library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.73.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RBufferedMatrix.c -o RBufferedMatrix.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init_package.c -o init_package.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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-x86_64/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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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
0.336 0.144 0.480
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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 480848 25.7 1056621 56.5 NA 634460 33.9
Vcells 891079 6.8 8388608 64.0 98304 2108715 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] "Thu Oct 23 19:49:53 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] "Thu Oct 23 19:49:54 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: 0x6000012e4000>
>
>
>
> 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] "Thu Oct 23 19:49:58 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] "Thu Oct 23 19:49:59 2025"
>
> ColMode(tmp2)
<pointer: 0x6000012e4000>
>
>
>
> ### 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,] 100.5478371 0.8749826 -1.0312119 0.3473313
[2,] -0.3984986 -1.9067837 -0.5906125 1.2603465
[3,] 0.7318010 0.4848122 -0.2239971 0.4402977
[4,] 0.2521542 -0.1030169 1.0957878 1.1560552
> 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 : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 100.5478371 0.8749826 1.0312119 0.3473313
[2,] 0.3984986 1.9067837 0.5906125 1.2603465
[3,] 0.7318010 0.4848122 0.2239971 0.4402977
[4,] 0.2521542 0.1030169 1.0957878 1.1560552
> 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 : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 10.0273544 0.9354050 1.0154861 0.5893482
[2,] 0.6312674 1.3808634 0.7685132 1.1226515
[3,] 0.8554537 0.6962846 0.4732833 0.6635493
[4,] 0.5021496 0.3209625 1.0467989 1.0752001
>
> 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 : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 225.82138 35.22903 36.18607 31.24081
[2,] 31.71117 40.71542 33.27574 37.48686
[3,] 34.28634 32.44766 29.95683 32.07579
[4,] 30.27365 28.31264 36.56378 36.90806
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x6000012a4300>
> exp(tmp5)
<pointer: 0x6000012a4300>
> log(tmp5,2)
<pointer: 0x6000012a4300>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 470.0176
> Min(tmp5)
[1] 52.92827
> mean(tmp5)
[1] 72.4217
> Sum(tmp5)
[1] 14484.34
> Var(tmp5)
[1] 868.1586
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 90.13293 68.56623 70.61145 69.48934 70.86670 71.86856 70.85751 73.36600
[9] 66.89839 71.55985
> rowSums(tmp5)
[1] 1802.659 1371.325 1412.229 1389.787 1417.334 1437.371 1417.150 1467.320
[9] 1337.968 1431.197
> rowVars(tmp5)
[1] 8032.93183 71.29112 49.58454 40.27090 76.98472 85.76745
[7] 117.43773 79.58219 71.36872 69.97913
> rowSd(tmp5)
[1] 89.626625 8.443407 7.041629 6.345935 8.774094 9.261072 10.836869
[8] 8.920885 8.448001 8.365353
> rowMax(tmp5)
[1] 470.01762 84.74381 86.61637 78.17565 90.79420 90.27833 93.04420
[8] 93.71815 81.11439 85.85242
> rowMin(tmp5)
[1] 58.02265 55.70114 61.64666 55.85407 58.93316 55.31710 52.92827 56.80578
[9] 53.39970 58.94209
>
> colMeans(tmp5)
[1] 113.04116 65.42517 72.68388 69.51648 68.52812 70.42726 69.14938
[8] 68.95881 73.57449 72.46327 68.16866 75.11840 65.13245 75.49840
[15] 71.48283 68.29239 73.87900 67.90800 67.26876 71.91703
> colSums(tmp5)
[1] 1130.4116 654.2517 726.8388 695.1648 685.2812 704.2726 691.4938
[8] 689.5881 735.7449 724.6327 681.6866 751.1840 651.3245 754.9840
[15] 714.8283 682.9239 738.7900 679.0800 672.6876 719.1703
> colVars(tmp5)
[1] 15793.04232 74.44942 55.68221 87.04236 60.87382 123.78067
[7] 45.29807 57.56414 75.83262 38.98736 71.56041 105.11901
[13] 19.60769 120.47180 88.52026 83.64035 13.25864 66.87573
[19] 41.52373 55.30345
> colSd(tmp5)
[1] 125.670372 8.628408 7.462051 9.329649 7.802168 11.125676
[7] 6.730384 7.587103 8.708193 6.243986 8.459339 10.252756
[13] 4.428057 10.975965 9.408520 9.145510 3.641242 8.177758
[19] 6.443891 7.436629
> colMax(tmp5)
[1] 470.01762 84.74381 84.36967 82.03198 82.28198 86.21479 78.11864
[8] 80.78276 90.27833 83.53033 82.89412 93.04420 72.01204 93.71815
[15] 87.27089 85.95887 80.16644 79.62698 78.46123 86.61637
> colMin(tmp5)
[1] 63.01064 54.74401 62.35122 55.31710 53.39970 53.30858 58.93316 56.80578
[9] 60.26044 63.67518 52.92827 55.85407 58.65265 59.86612 55.70114 56.44902
[17] 68.24724 58.02265 55.44232 64.00571
>
>
> ### 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] 90.13293 68.56623 70.61145 69.48934 70.86670 71.86856 70.85751 73.36600
[9] 66.89839 NA
> rowSums(tmp5)
[1] 1802.659 1371.325 1412.229 1389.787 1417.334 1437.371 1417.150 1467.320
[9] 1337.968 NA
> rowVars(tmp5)
[1] 8032.93183 71.29112 49.58454 40.27090 76.98472 85.76745
[7] 117.43773 79.58219 71.36872 72.18032
> rowSd(tmp5)
[1] 89.626625 8.443407 7.041629 6.345935 8.774094 9.261072 10.836869
[8] 8.920885 8.448001 8.495900
> rowMax(tmp5)
[1] 470.01762 84.74381 86.61637 78.17565 90.79420 90.27833 93.04420
[8] 93.71815 81.11439 NA
> rowMin(tmp5)
[1] 58.02265 55.70114 61.64666 55.85407 58.93316 55.31710 52.92827 56.80578
[9] 53.39970 NA
>
> colMeans(tmp5)
[1] 113.04116 65.42517 72.68388 69.51648 68.52812 70.42726 69.14938
[8] 68.95881 73.57449 72.46327 68.16866 75.11840 65.13245 75.49840
[15] 71.48283 68.29239 73.87900 NA 67.26876 71.91703
> colSums(tmp5)
[1] 1130.4116 654.2517 726.8388 695.1648 685.2812 704.2726 691.4938
[8] 689.5881 735.7449 724.6327 681.6866 751.1840 651.3245 754.9840
[15] 714.8283 682.9239 738.7900 NA 672.6876 719.1703
> colVars(tmp5)
[1] 15793.04232 74.44942 55.68221 87.04236 60.87382 123.78067
[7] 45.29807 57.56414 75.83262 38.98736 71.56041 105.11901
[13] 19.60769 120.47180 88.52026 83.64035 13.25864 NA
[19] 41.52373 55.30345
> colSd(tmp5)
[1] 125.670372 8.628408 7.462051 9.329649 7.802168 11.125676
[7] 6.730384 7.587103 8.708193 6.243986 8.459339 10.252756
[13] 4.428057 10.975965 9.408520 9.145510 3.641242 NA
[19] 6.443891 7.436629
> colMax(tmp5)
[1] 470.01762 84.74381 84.36967 82.03198 82.28198 86.21479 78.11864
[8] 80.78276 90.27833 83.53033 82.89412 93.04420 72.01204 93.71815
[15] 87.27089 85.95887 80.16644 NA 78.46123 86.61637
> colMin(tmp5)
[1] 63.01064 54.74401 62.35122 55.31710 53.39970 53.30858 58.93316 56.80578
[9] 60.26044 63.67518 52.92827 55.85407 58.65265 59.86612 55.70114 56.44902
[17] 68.24724 NA 55.44232 64.00571
>
> Max(tmp5,na.rm=TRUE)
[1] 470.0176
> Min(tmp5,na.rm=TRUE)
[1] 52.92827
> mean(tmp5,na.rm=TRUE)
[1] 72.39904
> Sum(tmp5,na.rm=TRUE)
[1] 14407.41
> Var(tmp5,na.rm=TRUE)
[1] 872.4401
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.13293 68.56623 70.61145 69.48934 70.86670 71.86856 70.85751 73.36600
[9] 66.89839 71.27720
> rowSums(tmp5,na.rm=TRUE)
[1] 1802.659 1371.325 1412.229 1389.787 1417.334 1437.371 1417.150 1467.320
[9] 1337.968 1354.267
> rowVars(tmp5,na.rm=TRUE)
[1] 8032.93183 71.29112 49.58454 40.27090 76.98472 85.76745
[7] 117.43773 79.58219 71.36872 72.18032
> rowSd(tmp5,na.rm=TRUE)
[1] 89.626625 8.443407 7.041629 6.345935 8.774094 9.261072 10.836869
[8] 8.920885 8.448001 8.495900
> rowMax(tmp5,na.rm=TRUE)
[1] 470.01762 84.74381 86.61637 78.17565 90.79420 90.27833 93.04420
[8] 93.71815 81.11439 85.85242
> rowMin(tmp5,na.rm=TRUE)
[1] 58.02265 55.70114 61.64666 55.85407 58.93316 55.31710 52.92827 56.80578
[9] 53.39970 58.94209
>
> colMeans(tmp5,na.rm=TRUE)
[1] 113.04116 65.42517 72.68388 69.51648 68.52812 70.42726 69.14938
[8] 68.95881 73.57449 72.46327 68.16866 75.11840 65.13245 75.49840
[15] 71.48283 68.29239 73.87900 66.90554 67.26876 71.91703
> colSums(tmp5,na.rm=TRUE)
[1] 1130.4116 654.2517 726.8388 695.1648 685.2812 704.2726 691.4938
[8] 689.5881 735.7449 724.6327 681.6866 751.1840 651.3245 754.9840
[15] 714.8283 682.9239 738.7900 602.1499 672.6876 719.1703
> colVars(tmp5,na.rm=TRUE)
[1] 15793.04232 74.44942 55.68221 87.04236 60.87382 123.78067
[7] 45.29807 57.56414 75.83262 38.98736 71.56041 105.11901
[13] 19.60769 120.47180 88.52026 83.64035 13.25864 63.92981
[19] 41.52373 55.30345
> colSd(tmp5,na.rm=TRUE)
[1] 125.670372 8.628408 7.462051 9.329649 7.802168 11.125676
[7] 6.730384 7.587103 8.708193 6.243986 8.459339 10.252756
[13] 4.428057 10.975965 9.408520 9.145510 3.641242 7.995612
[19] 6.443891 7.436629
> colMax(tmp5,na.rm=TRUE)
[1] 470.01762 84.74381 84.36967 82.03198 82.28198 86.21479 78.11864
[8] 80.78276 90.27833 83.53033 82.89412 93.04420 72.01204 93.71815
[15] 87.27089 85.95887 80.16644 79.62698 78.46123 86.61637
> colMin(tmp5,na.rm=TRUE)
[1] 63.01064 54.74401 62.35122 55.31710 53.39970 53.30858 58.93316 56.80578
[9] 60.26044 63.67518 52.92827 55.85407 58.65265 59.86612 55.70114 56.44902
[17] 68.24724 58.02265 55.44232 64.00571
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.13293 68.56623 70.61145 69.48934 70.86670 71.86856 70.85751 73.36600
[9] 66.89839 NaN
> rowSums(tmp5,na.rm=TRUE)
[1] 1802.659 1371.325 1412.229 1389.787 1417.334 1437.371 1417.150 1467.320
[9] 1337.968 0.000
> rowVars(tmp5,na.rm=TRUE)
[1] 8032.93183 71.29112 49.58454 40.27090 76.98472 85.76745
[7] 117.43773 79.58219 71.36872 NA
> rowSd(tmp5,na.rm=TRUE)
[1] 89.626625 8.443407 7.041629 6.345935 8.774094 9.261072 10.836869
[8] 8.920885 8.448001 NA
> rowMax(tmp5,na.rm=TRUE)
[1] 470.01762 84.74381 86.61637 78.17565 90.79420 90.27833 93.04420
[8] 93.71815 81.11439 NA
> rowMin(tmp5,na.rm=TRUE)
[1] 58.02265 55.70114 61.64666 55.85407 58.93316 55.31710 52.92827 56.80578
[9] 53.39970 NA
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 116.06213 66.00172 72.12384 70.30465 68.85221 71.70339 69.20351
[8] 68.68474 74.49052 72.06463 66.53250 74.38266 64.94132 76.82902
[15] 70.22237 68.46129 73.76193 NaN 66.02516 72.79606
> colSums(tmp5,na.rm=TRUE)
[1] 1044.5592 594.0155 649.1145 632.7419 619.6699 645.3305 622.8316
[8] 618.1627 670.4147 648.5817 598.7925 669.4439 584.4718 691.4612
[15] 632.0013 616.1516 663.8574 0.0000 594.2264 655.1646
> colVars(tmp5,na.rm=TRUE)
[1] 17664.50211 80.01596 59.11399 90.93403 67.30147 120.93256
[7] 50.92736 63.91461 75.87167 42.07302 50.38890 112.16902
[13] 21.64766 115.61228 81.71160 93.77447 14.76179 NA
[19] 29.31541 53.52348
> colSd(tmp5,na.rm=TRUE)
[1] 132.907871 8.945164 7.688562 9.535933 8.203747 10.996934
[7] 7.136341 7.994661 8.710435 6.486372 7.098514 10.590988
[13] 4.652704 10.752315 9.039447 9.683722 3.842108 NA
[19] 5.414370 7.315974
> colMax(tmp5,na.rm=TRUE)
[1] 470.01762 84.74381 84.36967 82.03198 82.28198 86.21479 78.11864
[8] 80.78276 90.27833 83.53033 74.63030 93.04420 72.01204 93.71815
[15] 87.27089 85.95887 80.16644 -Inf 73.26916 86.61637
> colMin(tmp5,na.rm=TRUE)
[1] 63.01064 54.74401 62.35122 55.31710 53.39970 53.30858 58.93316 56.80578
[9] 60.26044 63.67518 52.92827 55.85407 58.65265 59.86612 55.70114 56.44902
[17] 68.24724 Inf 55.44232 64.36205
>
>
>
>
> 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] 139.2069 148.4659 173.2918 101.1945 235.5962 215.4146 207.4809 203.1505
[9] 180.4955 143.7828
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 139.2069 148.4659 173.2918 101.1945 235.5962 215.4146 207.4809 203.1505
[9] 180.4955 143.7828
>
>
>
> 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 -8.526513e-14 -1.421085e-13 -2.842171e-14 -1.136868e-13
[6] 5.684342e-14 5.684342e-14 -2.842171e-13 -5.684342e-14 -8.526513e-14
[11] 5.684342e-14 -2.842171e-14 -5.684342e-14 1.989520e-13 0.000000e+00
[16] 2.842171e-14 -5.684342e-14 1.136868e-13 8.526513e-14 -1.136868e-13
>
>
>
>
>
>
>
>
>
>
> ## 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 19
1 18
7 2
10 11
7 1
9 3
10 14
6 10
5 3
4 8
9 8
6 17
8 1
3 1
7 1
1 19
3 19
2 14
1 13
9 18
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] 2.487515
> Min(tmp)
[1] -2.271122
> mean(tmp)
[1] 0.03777251
> Sum(tmp)
[1] 3.777251
> Var(tmp)
[1] 1.028335
>
> rowMeans(tmp)
[1] 0.03777251
> rowSums(tmp)
[1] 3.777251
> rowVars(tmp)
[1] 1.028335
> rowSd(tmp)
[1] 1.014068
> rowMax(tmp)
[1] 2.487515
> rowMin(tmp)
[1] -2.271122
>
> colMeans(tmp)
[1] -0.90287047 0.35284731 -0.82889849 0.03707469 0.05604672 0.48211669
[7] -0.76516164 1.73100613 -0.16114798 -0.58477294 0.26810598 -1.71216369
[13] 1.23287735 1.14130553 -0.24117402 0.28859147 -0.03785223 -0.90369186
[19] 0.21832148 -0.75076100 0.94746422 0.18502248 -0.32037664 0.50662569
[25] -1.25515735 0.19569647 0.82678703 0.15108041 -0.29899856 -0.49168795
[31] 0.32991024 -0.46246700 -1.00965820 -2.02719801 1.47171518 -2.27112177
[37] -0.89610571 -1.21171022 0.74896375 1.98942996 -0.21640642 -1.00738217
[43] 0.33266272 1.42753862 0.49429691 1.66314217 1.22807362 -1.42922118
[49] -0.46807710 0.92389351 1.06993014 -0.42977632 1.76165424 -0.52453518
[55] -0.20191172 0.94329945 0.40715244 -0.63445285 0.39947743 -0.61743652
[61] -0.97452140 0.11124565 -0.31332638 -1.55957869 0.35109431 0.73560443
[67] 1.21451085 0.43402317 0.79091102 -0.21963325 1.55318852 0.87012429
[73] -0.80655097 1.01438056 -1.88092061 0.65763449 2.31720726 -0.86009145
[79] 0.37886717 -1.45423318 0.09774476 -0.59980068 0.98791003 -0.65216713
[85] 0.80243050 -0.38473462 1.59707253 0.40978728 -0.22501543 -1.95185170
[91] 1.45057291 -0.66753745 -0.07637882 2.48751540 1.06581475 -1.58570652
[97] -1.38744329 -0.11945497 -0.50826008 -0.47311667
> colSums(tmp)
[1] -0.90287047 0.35284731 -0.82889849 0.03707469 0.05604672 0.48211669
[7] -0.76516164 1.73100613 -0.16114798 -0.58477294 0.26810598 -1.71216369
[13] 1.23287735 1.14130553 -0.24117402 0.28859147 -0.03785223 -0.90369186
[19] 0.21832148 -0.75076100 0.94746422 0.18502248 -0.32037664 0.50662569
[25] -1.25515735 0.19569647 0.82678703 0.15108041 -0.29899856 -0.49168795
[31] 0.32991024 -0.46246700 -1.00965820 -2.02719801 1.47171518 -2.27112177
[37] -0.89610571 -1.21171022 0.74896375 1.98942996 -0.21640642 -1.00738217
[43] 0.33266272 1.42753862 0.49429691 1.66314217 1.22807362 -1.42922118
[49] -0.46807710 0.92389351 1.06993014 -0.42977632 1.76165424 -0.52453518
[55] -0.20191172 0.94329945 0.40715244 -0.63445285 0.39947743 -0.61743652
[61] -0.97452140 0.11124565 -0.31332638 -1.55957869 0.35109431 0.73560443
[67] 1.21451085 0.43402317 0.79091102 -0.21963325 1.55318852 0.87012429
[73] -0.80655097 1.01438056 -1.88092061 0.65763449 2.31720726 -0.86009145
[79] 0.37886717 -1.45423318 0.09774476 -0.59980068 0.98791003 -0.65216713
[85] 0.80243050 -0.38473462 1.59707253 0.40978728 -0.22501543 -1.95185170
[91] 1.45057291 -0.66753745 -0.07637882 2.48751540 1.06581475 -1.58570652
[97] -1.38744329 -0.11945497 -0.50826008 -0.47311667
> 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] -0.90287047 0.35284731 -0.82889849 0.03707469 0.05604672 0.48211669
[7] -0.76516164 1.73100613 -0.16114798 -0.58477294 0.26810598 -1.71216369
[13] 1.23287735 1.14130553 -0.24117402 0.28859147 -0.03785223 -0.90369186
[19] 0.21832148 -0.75076100 0.94746422 0.18502248 -0.32037664 0.50662569
[25] -1.25515735 0.19569647 0.82678703 0.15108041 -0.29899856 -0.49168795
[31] 0.32991024 -0.46246700 -1.00965820 -2.02719801 1.47171518 -2.27112177
[37] -0.89610571 -1.21171022 0.74896375 1.98942996 -0.21640642 -1.00738217
[43] 0.33266272 1.42753862 0.49429691 1.66314217 1.22807362 -1.42922118
[49] -0.46807710 0.92389351 1.06993014 -0.42977632 1.76165424 -0.52453518
[55] -0.20191172 0.94329945 0.40715244 -0.63445285 0.39947743 -0.61743652
[61] -0.97452140 0.11124565 -0.31332638 -1.55957869 0.35109431 0.73560443
[67] 1.21451085 0.43402317 0.79091102 -0.21963325 1.55318852 0.87012429
[73] -0.80655097 1.01438056 -1.88092061 0.65763449 2.31720726 -0.86009145
[79] 0.37886717 -1.45423318 0.09774476 -0.59980068 0.98791003 -0.65216713
[85] 0.80243050 -0.38473462 1.59707253 0.40978728 -0.22501543 -1.95185170
[91] 1.45057291 -0.66753745 -0.07637882 2.48751540 1.06581475 -1.58570652
[97] -1.38744329 -0.11945497 -0.50826008 -0.47311667
> colMin(tmp)
[1] -0.90287047 0.35284731 -0.82889849 0.03707469 0.05604672 0.48211669
[7] -0.76516164 1.73100613 -0.16114798 -0.58477294 0.26810598 -1.71216369
[13] 1.23287735 1.14130553 -0.24117402 0.28859147 -0.03785223 -0.90369186
[19] 0.21832148 -0.75076100 0.94746422 0.18502248 -0.32037664 0.50662569
[25] -1.25515735 0.19569647 0.82678703 0.15108041 -0.29899856 -0.49168795
[31] 0.32991024 -0.46246700 -1.00965820 -2.02719801 1.47171518 -2.27112177
[37] -0.89610571 -1.21171022 0.74896375 1.98942996 -0.21640642 -1.00738217
[43] 0.33266272 1.42753862 0.49429691 1.66314217 1.22807362 -1.42922118
[49] -0.46807710 0.92389351 1.06993014 -0.42977632 1.76165424 -0.52453518
[55] -0.20191172 0.94329945 0.40715244 -0.63445285 0.39947743 -0.61743652
[61] -0.97452140 0.11124565 -0.31332638 -1.55957869 0.35109431 0.73560443
[67] 1.21451085 0.43402317 0.79091102 -0.21963325 1.55318852 0.87012429
[73] -0.80655097 1.01438056 -1.88092061 0.65763449 2.31720726 -0.86009145
[79] 0.37886717 -1.45423318 0.09774476 -0.59980068 0.98791003 -0.65216713
[85] 0.80243050 -0.38473462 1.59707253 0.40978728 -0.22501543 -1.95185170
[91] 1.45057291 -0.66753745 -0.07637882 2.48751540 1.06581475 -1.58570652
[97] -1.38744329 -0.11945497 -0.50826008 -0.47311667
> colMedians(tmp)
[1] -0.90287047 0.35284731 -0.82889849 0.03707469 0.05604672 0.48211669
[7] -0.76516164 1.73100613 -0.16114798 -0.58477294 0.26810598 -1.71216369
[13] 1.23287735 1.14130553 -0.24117402 0.28859147 -0.03785223 -0.90369186
[19] 0.21832148 -0.75076100 0.94746422 0.18502248 -0.32037664 0.50662569
[25] -1.25515735 0.19569647 0.82678703 0.15108041 -0.29899856 -0.49168795
[31] 0.32991024 -0.46246700 -1.00965820 -2.02719801 1.47171518 -2.27112177
[37] -0.89610571 -1.21171022 0.74896375 1.98942996 -0.21640642 -1.00738217
[43] 0.33266272 1.42753862 0.49429691 1.66314217 1.22807362 -1.42922118
[49] -0.46807710 0.92389351 1.06993014 -0.42977632 1.76165424 -0.52453518
[55] -0.20191172 0.94329945 0.40715244 -0.63445285 0.39947743 -0.61743652
[61] -0.97452140 0.11124565 -0.31332638 -1.55957869 0.35109431 0.73560443
[67] 1.21451085 0.43402317 0.79091102 -0.21963325 1.55318852 0.87012429
[73] -0.80655097 1.01438056 -1.88092061 0.65763449 2.31720726 -0.86009145
[79] 0.37886717 -1.45423318 0.09774476 -0.59980068 0.98791003 -0.65216713
[85] 0.80243050 -0.38473462 1.59707253 0.40978728 -0.22501543 -1.95185170
[91] 1.45057291 -0.66753745 -0.07637882 2.48751540 1.06581475 -1.58570652
[97] -1.38744329 -0.11945497 -0.50826008 -0.47311667
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.9028705 0.3528473 -0.8288985 0.03707469 0.05604672 0.4821167 -0.7651616
[2,] -0.9028705 0.3528473 -0.8288985 0.03707469 0.05604672 0.4821167 -0.7651616
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 1.731006 -0.161148 -0.5847729 0.268106 -1.712164 1.232877 1.141306
[2,] 1.731006 -0.161148 -0.5847729 0.268106 -1.712164 1.232877 1.141306
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -0.241174 0.2885915 -0.03785223 -0.9036919 0.2183215 -0.750761 0.9474642
[2,] -0.241174 0.2885915 -0.03785223 -0.9036919 0.2183215 -0.750761 0.9474642
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 0.1850225 -0.3203766 0.5066257 -1.255157 0.1956965 0.826787 0.1510804
[2,] 0.1850225 -0.3203766 0.5066257 -1.255157 0.1956965 0.826787 0.1510804
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] -0.2989986 -0.491688 0.3299102 -0.462467 -1.009658 -2.027198 1.471715
[2,] -0.2989986 -0.491688 0.3299102 -0.462467 -1.009658 -2.027198 1.471715
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -2.271122 -0.8961057 -1.21171 0.7489638 1.98943 -0.2164064 -1.007382
[2,] -2.271122 -0.8961057 -1.21171 0.7489638 1.98943 -0.2164064 -1.007382
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 0.3326627 1.427539 0.4942969 1.663142 1.228074 -1.429221 -0.4680771
[2,] 0.3326627 1.427539 0.4942969 1.663142 1.228074 -1.429221 -0.4680771
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.9238935 1.06993 -0.4297763 1.761654 -0.5245352 -0.2019117 0.9432995
[2,] 0.9238935 1.06993 -0.4297763 1.761654 -0.5245352 -0.2019117 0.9432995
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 0.4071524 -0.6344529 0.3994774 -0.6174365 -0.9745214 0.1112457 -0.3133264
[2,] 0.4071524 -0.6344529 0.3994774 -0.6174365 -0.9745214 0.1112457 -0.3133264
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] -1.559579 0.3510943 0.7356044 1.214511 0.4340232 0.790911 -0.2196333
[2,] -1.559579 0.3510943 0.7356044 1.214511 0.4340232 0.790911 -0.2196333
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] 1.553189 0.8701243 -0.806551 1.014381 -1.880921 0.6576345 2.317207
[2,] 1.553189 0.8701243 -0.806551 1.014381 -1.880921 0.6576345 2.317207
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] -0.8600915 0.3788672 -1.454233 0.09774476 -0.5998007 0.98791 -0.6521671
[2,] -0.8600915 0.3788672 -1.454233 0.09774476 -0.5998007 0.98791 -0.6521671
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] 0.8024305 -0.3847346 1.597073 0.4097873 -0.2250154 -1.951852 1.450573
[2,] 0.8024305 -0.3847346 1.597073 0.4097873 -0.2250154 -1.951852 1.450573
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -0.6675374 -0.07637882 2.487515 1.065815 -1.585707 -1.387443 -0.119455
[2,] -0.6675374 -0.07637882 2.487515 1.065815 -1.585707 -1.387443 -0.119455
[,99] [,100]
[1,] -0.5082601 -0.4731167
[2,] -0.5082601 -0.4731167
>
>
> Max(tmp2)
[1] 3.185547
> Min(tmp2)
[1] -2.115573
> mean(tmp2)
[1] 0.1309773
> Sum(tmp2)
[1] 13.09773
> Var(tmp2)
[1] 1.049724
>
> rowMeans(tmp2)
[1] 0.248840638 -0.408873967 -0.596148641 1.045601659 -0.037613205
[6] -1.889953364 0.182464264 1.050490644 3.185546591 0.348120460
[11] 1.609630593 0.502036318 0.657196959 -1.562853505 -0.019234321
[16] -1.392176586 -0.860043915 -1.128422001 1.241736852 -0.300668723
[21] -0.143225614 -0.863354309 1.341055600 -0.373158226 -0.083084934
[26] 1.267946697 0.131490180 1.156120288 -0.296191294 -0.272146638
[31] 0.860287723 -0.192301528 -0.214767413 0.172572679 -1.058481446
[36] -0.208935106 1.195089297 -0.901351197 -0.104518795 -0.720509509
[41] -1.135694884 0.209003642 0.428793851 0.455247368 -1.228344237
[46] 1.404521707 -1.537775528 -1.347822300 1.266715970 0.056067384
[51] 0.135763226 1.030351209 1.625995125 -0.861080982 1.038564851
[56] -1.134546380 1.144514638 1.195193505 1.072413774 -2.115573500
[61] -0.673034371 -0.064428871 1.368383680 0.007006474 0.061846354
[66] -0.121775811 0.352034927 -1.426095992 1.816324240 0.816251184
[71] 1.547072411 -0.489445902 -0.862476140 -1.809649696 -0.100804634
[76] 1.536297774 0.608904488 2.444944510 1.104436246 -1.779804936
[81] -0.735950733 0.956962061 0.481262373 -0.546057804 1.781648041
[86] 0.050011823 0.012331823 1.018713534 -0.516224011 -0.703314679
[91] 1.165767758 0.558530197 -0.657382035 1.208871710 -0.065155270
[96] -0.877859429 0.419913700 0.565142590 -0.433705162 0.807719074
> rowSums(tmp2)
[1] 0.248840638 -0.408873967 -0.596148641 1.045601659 -0.037613205
[6] -1.889953364 0.182464264 1.050490644 3.185546591 0.348120460
[11] 1.609630593 0.502036318 0.657196959 -1.562853505 -0.019234321
[16] -1.392176586 -0.860043915 -1.128422001 1.241736852 -0.300668723
[21] -0.143225614 -0.863354309 1.341055600 -0.373158226 -0.083084934
[26] 1.267946697 0.131490180 1.156120288 -0.296191294 -0.272146638
[31] 0.860287723 -0.192301528 -0.214767413 0.172572679 -1.058481446
[36] -0.208935106 1.195089297 -0.901351197 -0.104518795 -0.720509509
[41] -1.135694884 0.209003642 0.428793851 0.455247368 -1.228344237
[46] 1.404521707 -1.537775528 -1.347822300 1.266715970 0.056067384
[51] 0.135763226 1.030351209 1.625995125 -0.861080982 1.038564851
[56] -1.134546380 1.144514638 1.195193505 1.072413774 -2.115573500
[61] -0.673034371 -0.064428871 1.368383680 0.007006474 0.061846354
[66] -0.121775811 0.352034927 -1.426095992 1.816324240 0.816251184
[71] 1.547072411 -0.489445902 -0.862476140 -1.809649696 -0.100804634
[76] 1.536297774 0.608904488 2.444944510 1.104436246 -1.779804936
[81] -0.735950733 0.956962061 0.481262373 -0.546057804 1.781648041
[86] 0.050011823 0.012331823 1.018713534 -0.516224011 -0.703314679
[91] 1.165767758 0.558530197 -0.657382035 1.208871710 -0.065155270
[96] -0.877859429 0.419913700 0.565142590 -0.433705162 0.807719074
> 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] 0.248840638 -0.408873967 -0.596148641 1.045601659 -0.037613205
[6] -1.889953364 0.182464264 1.050490644 3.185546591 0.348120460
[11] 1.609630593 0.502036318 0.657196959 -1.562853505 -0.019234321
[16] -1.392176586 -0.860043915 -1.128422001 1.241736852 -0.300668723
[21] -0.143225614 -0.863354309 1.341055600 -0.373158226 -0.083084934
[26] 1.267946697 0.131490180 1.156120288 -0.296191294 -0.272146638
[31] 0.860287723 -0.192301528 -0.214767413 0.172572679 -1.058481446
[36] -0.208935106 1.195089297 -0.901351197 -0.104518795 -0.720509509
[41] -1.135694884 0.209003642 0.428793851 0.455247368 -1.228344237
[46] 1.404521707 -1.537775528 -1.347822300 1.266715970 0.056067384
[51] 0.135763226 1.030351209 1.625995125 -0.861080982 1.038564851
[56] -1.134546380 1.144514638 1.195193505 1.072413774 -2.115573500
[61] -0.673034371 -0.064428871 1.368383680 0.007006474 0.061846354
[66] -0.121775811 0.352034927 -1.426095992 1.816324240 0.816251184
[71] 1.547072411 -0.489445902 -0.862476140 -1.809649696 -0.100804634
[76] 1.536297774 0.608904488 2.444944510 1.104436246 -1.779804936
[81] -0.735950733 0.956962061 0.481262373 -0.546057804 1.781648041
[86] 0.050011823 0.012331823 1.018713534 -0.516224011 -0.703314679
[91] 1.165767758 0.558530197 -0.657382035 1.208871710 -0.065155270
[96] -0.877859429 0.419913700 0.565142590 -0.433705162 0.807719074
> rowMin(tmp2)
[1] 0.248840638 -0.408873967 -0.596148641 1.045601659 -0.037613205
[6] -1.889953364 0.182464264 1.050490644 3.185546591 0.348120460
[11] 1.609630593 0.502036318 0.657196959 -1.562853505 -0.019234321
[16] -1.392176586 -0.860043915 -1.128422001 1.241736852 -0.300668723
[21] -0.143225614 -0.863354309 1.341055600 -0.373158226 -0.083084934
[26] 1.267946697 0.131490180 1.156120288 -0.296191294 -0.272146638
[31] 0.860287723 -0.192301528 -0.214767413 0.172572679 -1.058481446
[36] -0.208935106 1.195089297 -0.901351197 -0.104518795 -0.720509509
[41] -1.135694884 0.209003642 0.428793851 0.455247368 -1.228344237
[46] 1.404521707 -1.537775528 -1.347822300 1.266715970 0.056067384
[51] 0.135763226 1.030351209 1.625995125 -0.861080982 1.038564851
[56] -1.134546380 1.144514638 1.195193505 1.072413774 -2.115573500
[61] -0.673034371 -0.064428871 1.368383680 0.007006474 0.061846354
[66] -0.121775811 0.352034927 -1.426095992 1.816324240 0.816251184
[71] 1.547072411 -0.489445902 -0.862476140 -1.809649696 -0.100804634
[76] 1.536297774 0.608904488 2.444944510 1.104436246 -1.779804936
[81] -0.735950733 0.956962061 0.481262373 -0.546057804 1.781648041
[86] 0.050011823 0.012331823 1.018713534 -0.516224011 -0.703314679
[91] 1.165767758 0.558530197 -0.657382035 1.208871710 -0.065155270
[96] -0.877859429 0.419913700 0.565142590 -0.433705162 0.807719074
>
> colMeans(tmp2)
[1] 0.1309773
> colSums(tmp2)
[1] 13.09773
> colVars(tmp2)
[1] 1.049724
> colSd(tmp2)
[1] 1.02456
> colMax(tmp2)
[1] 3.185547
> colMin(tmp2)
[1] -2.115573
> colMedians(tmp2)
[1] 0.0530396
> colRanges(tmp2)
[,1]
[1,] -2.115573
[2,] 3.185547
>
> 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] 1.47283506 0.09938974 3.31623992 -0.03625166 3.07126075 -4.06869117
[7] 0.70843837 5.11153118 1.75496839 -0.33277842
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.1970611
[2,] -0.7022634
[3,] -0.1595201
[4,] 1.0565498
[5,] 1.8032590
>
> rowApply(tmp,sum)
[1] 1.2712229 2.4087024 -2.2947516 1.4872039 2.5507423 1.2961975
[7] 1.7350563 0.3699517 2.2509972 0.0216196
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 3 3 10 2 10 10 10 2 1 5
[2,] 1 9 5 4 4 8 2 7 5 8
[3,] 10 8 3 10 6 5 3 9 6 1
[4,] 2 10 8 3 2 6 6 4 8 2
[5,] 9 7 9 6 7 7 4 5 3 6
[6,] 4 4 1 5 5 3 1 1 9 4
[7,] 7 2 4 8 3 2 5 10 2 7
[8,] 8 1 7 7 8 4 9 6 10 9
[9,] 5 5 2 9 9 1 8 8 4 10
[10,] 6 6 6 1 1 9 7 3 7 3
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -3.37444060 1.97038773 0.92698669 -2.48791231 -4.17435132 1.06031828
[7] 0.24500333 -2.38182383 -1.64796251 1.53199994 0.05897746 -2.71142749
[13] -1.56443809 5.38423326 -3.51369412 -1.73246595 -1.53146887 2.66763601
[19] -0.30401594 1.57170680
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.5149108636
[2,] -1.3882765615
[3,] -1.3650830516
[4,] 0.0008617179
[5,] 0.8929681624
>
> rowApply(tmp,sum)
[1] -2.07993726 -9.56539097 -0.03410332 0.61960769 1.05307233
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 4 14 1 3 17
[2,] 12 9 18 18 4
[3,] 5 16 10 7 20
[4,] 10 7 5 8 9
[5,] 7 3 2 11 6
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -1.3882765615 0.3781846 -1.12236299 -0.3464540 -1.0603577 1.5881741
[2,] 0.0008617179 -0.6430383 0.37358779 -1.1006706 -1.5621356 -0.1559635
[3,] -1.3650830516 1.1296600 0.01278887 -0.5172741 -1.2490361 -0.2366612
[4,] -1.5149108636 1.7557577 -0.54966341 -0.2700668 0.2736160 0.5104886
[5,] 0.8929681624 -0.6501763 2.21263642 -0.2534468 -0.5764381 -0.6457197
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 1.3372147 -2.48963494 -2.33523365 -0.1832274 0.71924229 0.7155598
[2,] -1.6311532 0.43138564 -0.51667472 -1.6397646 0.66577530 -0.9009823
[3,] 1.1844840 0.01386105 1.37793074 0.7796778 0.04869706 -1.0998107
[4,] 0.3657746 -0.67262434 -0.11087809 1.7526914 -2.60124619 -0.7697600
[5,] -1.0113168 0.33518876 -0.06310677 0.8226227 1.22650901 -0.6564342
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -1.4307394 2.8003422 -0.76856986 -1.0699352 -0.4078150 1.77042990
[2,] -0.4792029 -1.5494883 -1.38116785 0.9107850 0.3392184 0.58781377
[3,] -0.9840943 0.7985624 0.02385585 -0.1561299 -0.1219082 -0.06599457
[4,] 1.7857420 2.2622660 -1.00059432 0.7204038 -2.1510826 0.33379096
[5,] -0.4561435 1.0725509 -0.38721794 -2.1375897 0.8101186 0.04159596
[,19] [,20]
[1,] 0.61486668 0.59865510
[2,] -1.30079870 -0.01377806
[3,] 0.05529079 0.33708020
[4,] 0.37906618 0.12083702
[5,] -0.05244089 0.52891254
>
>
> 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 : 654 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 : 566 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 1.594943 0.941872 -1.065794 -0.2141304 0.3105614 0.1853977 0.9046362
col8 col9 col10 col11 col12 col13 col14
row1 1.861294 0.6166093 0.346799 -0.7485064 -0.3688432 0.04997149 -1.759944
col15 col16 col17 col18 col19 col20
row1 0.9969174 -0.9988823 0.2824665 -0.521472 -1.02472 -1.997528
> tmp[,"col10"]
col10
row1 0.3467990
row2 0.2171045
row3 0.4163749
row4 -1.2393898
row5 -0.7695958
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 1.59494255 0.941872 -1.0657935 -0.2141304 0.3105614 0.1853977 0.9046362
row5 0.07504866 2.232622 0.6575819 -0.9806116 1.5807834 -0.3399457 -0.9859912
col8 col9 col10 col11 col12 col13 col14
row1 1.8612940 0.6166093 0.3467990 -0.7485064 -0.3688432 0.04997149 -1.759944
row5 0.4235093 0.8688538 -0.7695958 1.1802118 -0.9041583 0.27169971 -1.070238
col15 col16 col17 col18 col19 col20
row1 0.99691742 -0.9988823 0.2824665 -0.5214720 -1.02472 -1.9975282
row5 -0.00018016 0.6865384 -0.3581402 -0.1684826 1.20371 -0.3263458
> tmp[,c("col6","col20")]
col6 col20
row1 0.1853977 -1.9975282
row2 -0.2241510 1.0664005
row3 0.9212025 -0.8403772
row4 -0.4365743 2.0138969
row5 -0.3399457 -0.3263458
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.1853977 -1.9975282
row5 -0.3399457 -0.3263458
>
>
>
>
> 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 48.78427 50.06355 50.03719 50.09459 49.37663 104.9808 49.79479 49.72661
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.03449 49.563 49.27125 50.24699 50.84155 50.37653 50.28265 48.48602
col17 col18 col19 col20
row1 50.44987 49.5337 50.43454 104.2874
> tmp[,"col10"]
col10
row1 49.56300
row2 30.28676
row3 29.61827
row4 29.82967
row5 50.09346
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 48.78427 50.06355 50.03719 50.09459 49.37663 104.9808 49.79479 49.72661
row5 48.81848 49.78104 50.89934 50.79583 50.32044 104.1732 51.50710 51.09256
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.03449 49.56300 49.27125 50.24699 50.84155 50.37653 50.28265 48.48602
row5 50.32358 50.09346 48.28800 51.21872 48.77067 51.63362 49.32695 50.18257
col17 col18 col19 col20
row1 50.44987 49.53370 50.43454 104.2874
row5 49.17984 50.21674 49.18057 103.4411
> tmp[,c("col6","col20")]
col6 col20
row1 104.98080 104.28742
row2 76.72428 75.25290
row3 74.92599 73.30623
row4 75.08003 72.93178
row5 104.17325 103.44112
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 104.9808 104.2874
row5 104.1732 103.4411
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 104.9808 104.2874
row5 104.1732 103.4411
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -0.8327887
[2,] -1.1851628
[3,] 0.4218791
[4,] 0.0405425
[5,] 0.4002786
> tmp[,c("col17","col7")]
col17 col7
[1,] 1.7328352 1.1683005
[2,] -0.9411953 1.2124209
[3,] -1.1061667 -0.7643607
[4,] -0.3488518 0.1389985
[5,] 0.6826849 0.7146457
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.3529212 -1.8042952
[2,] 1.4630871 0.4085798
[3,] 0.6417615 0.7194042
[4,] -0.4561440 -1.0948428
[5,] -0.5164132 0.9342489
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.3529212
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.3529212
[2,] 1.4630871
>
>
>
> 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] [,7]
row3 0.5743954 -0.67225687 1.7492786 0.1726928 1.530392 0.6518495 -1.4054158
row1 0.1701057 0.06501907 -0.2067499 1.5305612 1.715019 0.7967479 -0.4492746
[,8] [,9] [,10] [,11] [,12] [,13]
row3 -0.3728570 -1.3790961 0.5475004 -1.1493399 -0.3044534 0.7475198
row1 -0.3831365 -0.9929765 0.1559940 -0.3793817 0.1766553 -0.2547157
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row3 -0.8246722 0.7737047 0.2657382 1.5087105 0.1595589 1.1605875 -0.5379114
row1 1.5154463 0.2990620 -0.2608680 -0.8539336 0.2674354 -0.4428823 1.1870177
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -0.9402847 -1.498757 2.050579 0.3840688 -1.060156 -0.7741152 -0.5863667
[,8] [,9] [,10]
row2 0.2525752 -0.4020415 -1.542485
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.6549069 1.208672 -0.8715356 -0.03538667 0.03988461 -0.09627284 1.56193
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.1756999 -0.5268368 0.8246704 0.2068508 0.4738723 1.261676 1.388103
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.7882521 -0.5046599 0.1835293 0.7516936 -0.3628447 -1.270817
>
>
> 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: 0x6000012ec060>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1167949e2389f"
[2] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1167922f3749e"
[3] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM116791d6d42ff"
[4] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1167970498270"
[5] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM116796a12c0a7"
[6] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1167975264a58"
[7] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1167924db137e"
[8] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM116792adcc819"
[9] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM116794d4f74b"
[10] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1167939b75f67"
[11] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1167935d880cb"
[12] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1167918efab0b"
[13] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM116791ec66bf7"
[14] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1167974da34e9"
[15] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1167921c7e8ee"
>
>
> ### 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: 0x60000123c180>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x60000123c180>
Warning message:
In dir.create(new.directory) :
'/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x60000123c180>
> rowMedians(tmp)
[1] 0.024856709 -0.270597135 0.018262789 -0.012742835 0.201490943
[6] -0.292302305 -0.006914134 0.128567813 0.066684723 0.038333924
[11] 0.118108084 -0.200214199 0.770122217 -0.325717185 0.806921669
[16] -0.154152076 -0.355902524 0.322894816 -0.076930878 -0.143009381
[21] 0.033922383 -0.124141325 -0.458728492 -0.096618578 -0.399431249
[26] 0.438006668 0.519757369 -0.040574967 -0.249545426 -0.219404314
[31] -0.270711443 -0.046368162 -0.331654605 0.050860629 0.213185098
[36] -0.455960277 0.051269373 -0.498442870 -0.363512263 -0.069572882
[41] -0.006294277 -0.263189896 0.405208356 0.119564923 -0.086704554
[46] 0.321898692 -0.011488369 0.242082044 0.392146998 -0.381986810
[51] 0.608082826 -0.209752358 -0.155463050 0.330038049 -0.141108533
[56] -0.036245467 -0.604819106 0.464832156 -0.624425393 0.016048388
[61] 0.266661461 -0.408057432 0.406197082 -0.173551407 -0.387520593
[66] 0.036761536 0.122689515 -0.193397452 -0.157488525 0.115360296
[71] 0.090938727 0.240758768 -0.451843198 0.054307566 0.108861316
[76] 0.040202589 -0.265420128 -0.137547314 -0.103978879 -0.186557016
[81] -0.230185058 -0.328306072 0.168356588 -0.281494425 -0.177140499
[86] 0.681710573 -0.484847829 0.018534831 -0.117995467 0.046965583
[91] -0.331982893 0.022566339 -0.061460068 0.013712513 0.655984393
[96] 0.401511167 -0.084824196 0.482477969 -0.475084122 0.120899592
[101] -0.218972244 -0.462427188 0.024967211 -0.241483722 0.235345581
[106] -0.152268772 -0.259524778 -0.233100051 -0.054566384 -0.065766594
[111] -0.012467217 0.465963167 -0.437057209 -0.170716502 0.332390982
[116] 0.027728440 0.454761862 -0.523598860 -0.142777931 0.025886221
[121] 0.358782907 0.350975043 0.535598301 -0.339116748 -0.344046974
[126] 0.828059796 -0.067278310 0.238343990 -0.760576244 -0.522847244
[131] -0.541333513 0.520945274 0.442032758 -0.090735728 -0.081139022
[136] -0.436707115 0.267773582 0.194154274 -0.122821061 0.044401168
[141] 0.266631574 -0.102514467 -0.178237795 0.280487743 0.261098208
[146] 0.089585455 -0.199023395 0.247411636 -0.236270148 0.454331655
[151] -0.125985595 0.351428016 -0.462187743 0.112850300 -0.149565870
[156] -0.046051213 0.546537881 0.319798097 0.048769561 0.285316596
[161] -0.097768515 -0.228189981 -0.462376393 0.171892115 -0.322832653
[166] 0.381486903 -0.411148247 -0.090284313 0.556520122 -0.472058207
[171] -0.285253626 -0.142753921 -0.211952992 0.158956154 0.252144123
[176] -0.635410174 0.438745403 0.411010227 -0.222607360 0.201479532
[181] -0.209450430 0.189200517 -0.628216747 0.230742843 0.025443056
[186] -0.086070890 -0.456137588 -0.601812322 0.131447135 -0.411556109
[191] -0.379060198 -0.278393919 -0.325755615 -0.280169130 0.087202453
[196] 0.113667849 0.089351682 -0.502295249 -0.317001969 0.291748276
[201] -0.066095261 0.415475841 -0.265558241 -0.159209795 -0.223602951
[206] -0.275489700 -0.555293843 0.088350348 -0.119833042 -0.116720028
[211] -0.022181277 -0.271323010 -0.191364097 0.147743337 0.366791311
[216] 0.371147488 -0.188958458 -0.087167775 -0.214564414 0.194844687
[221] 0.150126890 0.357661285 -0.466946706 -0.182030377 -0.319869159
[226] -0.651089611 -0.116429130 0.263908904 -0.014566202 0.288674020
>
> proc.time()
user system elapsed
2.460 13.955 16.806
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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: 0x6000038b00c0>
> .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: 0x6000038b00c0>
> .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: 0x6000038b00c0>
> .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: 0x6000038b00c0>
> 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: 0x6000038ac000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000038ac000>
> .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: 0x6000038ac000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000038ac000>
> .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: 0x6000038ac000>
> 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: 0x6000038ac180>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000038ac180>
> .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: 0x6000038ac180>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x6000038ac180>
> .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: 0x6000038ac180>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x6000038ac180>
> .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: 0x6000038ac180>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x6000038ac180>
> .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: 0x6000038ac180>
> 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: 0x6000038e4120>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x6000038e4120>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000038e4120>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000038e4120>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile119d3142cc4fe" "BufferedMatrixFile119d37390a0b"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile119d3142cc4fe" "BufferedMatrixFile119d37390a0b"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000038e4360>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000038e4360>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x6000038e4360>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x6000038e4360>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x6000038e4360>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x6000038e4360>
> .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: 0x6000038b0180>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000038b0180>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x6000038b0180>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x6000038b0180>
> 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: 0x6000038a8000>
> .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: 0x6000038a8000>
> rm(P)
>
> proc.time()
user system elapsed
0.322 0.152 0.475
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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
0.299 0.085 0.382