Ben Bolstad
| Snapshot Date: 2025-12-29 13:45 -0500 (Mon, 29 Dec 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 2026-01-01 11:58 -0500 (Thu, 01 Jan 2026).
| 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" | 4883 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 | | ||||||||
| 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BufferedMatrix |
| Version: 1.74.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BufferedMatrix_1.74.0.tar.gz |
| StartedAt: 2025-12-30 09:00:03 -0000 (Tue, 30 Dec 2025) |
| EndedAt: 2025-12-30 09:00:32 -0000 (Tue, 30 Dec 2025) |
| EllapsedTime: 29.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BufferedMatrix_1.74.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 ... OK
* used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* 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 loading without being on the library search path ... 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 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.74.0’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c RBufferedMatrix.c -o RBufferedMatrix.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c: In function ‘dbm_ReadOnlyMode’:
doubleBufferedMatrix.c:1580:7: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses]
1580 | if (!(Matrix->readonly) & setting){
| ^~~~~~~~~~~~~~~~~~~
doubleBufferedMatrix.c: At top level:
doubleBufferedMatrix.c:3327:12: warning: ‘sort_double’ defined but not used [-Wunused-function]
3327 | static int sort_double(const double *a1,const double *a2){
| ^~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c init_package.c -o init_package.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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
0.335 0.029 0.350
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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] "/home/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) max used (Mb)
Ncells 478398 25.6 1047041 56 639620 34.2
Vcells 885166 6.8 8388608 64 2080985 15.9
>
>
>
>
> ##
> ## 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 Dec 30 09:00:27 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 Dec 30 09:00:27 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: 0xfb48ff0>
>
>
>
> 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 Dec 30 09:00:27 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 Dec 30 09:00:27 2025"
>
> ColMode(tmp2)
<pointer: 0xfb48ff0>
>
>
>
> ### 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,] 100.2928445 0.22847568 0.5840600 -1.2839226
[2,] 0.5034144 -0.89343748 0.9393734 0.9550614
[3,] -1.2172819 -0.80021082 0.3537694 -0.1151632
[4,] 0.8045501 -0.04405633 -1.1154515 1.2279528
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/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,] 100.2928445 0.22847568 0.5840600 1.2839226
[2,] 0.5034144 0.89343748 0.9393734 0.9550614
[3,] 1.2172819 0.80021082 0.3537694 0.1151632
[4,] 0.8045501 0.04405633 1.1154515 1.2279528
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/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,] 10.0146315 0.4779913 0.7642382 1.1331031
[2,] 0.7095170 0.9452182 0.9692128 0.9772725
[3,] 1.1033050 0.8945450 0.5947852 0.3393571
[4,] 0.8969672 0.2098960 1.0561494 1.1081303
>
> 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: /home/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,] 225.43916 30.00839 33.22644 37.61495
[2,] 32.59858 35.34562 35.63150 35.72779
[3,] 37.25033 34.74566 31.30162 28.50873
[4,] 34.77422 27.14302 36.67695 37.30926
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0xe82b6c0>
> exp(tmp5)
<pointer: 0xe82b6c0>
> log(tmp5,2)
<pointer: 0xe82b6c0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 469.2221
> Min(tmp5)
[1] 52.58092
> mean(tmp5)
[1] 72.52231
> Sum(tmp5)
[1] 14504.46
> Var(tmp5)
[1] 864.6242
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 90.72212 69.14627 67.63177 71.36113 71.87590 72.55954 71.95200 68.82918
[9] 69.19225 71.95294
> rowSums(tmp5)
[1] 1814.442 1382.925 1352.635 1427.223 1437.518 1451.191 1439.040 1376.584
[9] 1383.845 1439.059
> rowVars(tmp5)
[1] 8013.10251 33.12335 88.01251 49.21381 109.62125 99.89649
[7] 54.63234 55.12019 77.56607 61.09827
> rowSd(tmp5)
[1] 89.515934 5.755289 9.381499 7.015255 10.470017 9.994823 7.391369
[8] 7.424298 8.807160 7.816538
> rowMax(tmp5)
[1] 469.22207 81.42224 80.38018 81.63478 95.78084 88.40061 89.30328
[8] 86.31748 88.71141 85.20387
> rowMin(tmp5)
[1] 56.96644 58.08829 52.58092 56.49463 55.01190 55.10450 58.69443 55.53874
[9] 55.95298 57.63078
>
> colMeans(tmp5)
[1] 117.57285 70.88997 71.01478 70.05532 66.00020 72.05605 68.98571
[8] 68.71573 73.31011 67.11115 71.87044 71.84411 67.23595 70.33891
[15] 69.35920 69.06970 70.62622 70.00729 71.14182 73.24068
> colSums(tmp5)
[1] 1175.7285 708.8997 710.1478 700.5532 660.0020 720.5605 689.8571
[8] 687.1573 733.1011 671.1115 718.7044 718.4411 672.3595 703.3891
[15] 693.5920 690.6970 706.2622 700.0729 711.4182 732.4068
> colVars(tmp5)
[1] 15333.63609 63.95686 19.41159 65.74688 55.94613 93.33403
[7] 69.07837 53.52070 162.80355 99.70968 45.21561 48.72134
[13] 49.37300 87.97596 114.52174 28.50226 62.34270 64.76243
[19] 67.76787 78.03740
> colSd(tmp5)
[1] 123.829060 7.997303 4.405858 8.108445 7.479715 9.660954
[7] 8.311340 7.315785 12.759449 9.985474 6.724255 6.980067
[13] 7.026592 9.379550 10.701483 5.338751 7.895740 8.047511
[19] 8.232124 8.833878
> colMax(tmp5)
[1] 469.22207 86.94047 77.74338 78.29060 78.79620 95.44749 78.50201
[8] 79.83907 89.30328 83.81080 80.98352 81.66167 80.23727 81.42224
[15] 87.18237 75.32785 85.20387 80.22414 86.31748 88.71141
> colMin(tmp5)
[1] 67.84968 56.49463 65.15022 57.99942 56.50041 58.79383 55.95298 53.65054
[9] 55.53874 52.58092 61.77068 59.10162 59.74671 55.01190 56.96644 60.39909
[17] 61.46240 55.01958 58.14643 62.22334
>
>
> ### 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] 90.72212 69.14627 67.63177 71.36113 71.87590 72.55954 71.95200 68.82918
[9] 69.19225 NA
> rowSums(tmp5)
[1] 1814.442 1382.925 1352.635 1427.223 1437.518 1451.191 1439.040 1376.584
[9] 1383.845 NA
> rowVars(tmp5)
[1] 8013.10251 33.12335 88.01251 49.21381 109.62125 99.89649
[7] 54.63234 55.12019 77.56607 64.22756
> rowSd(tmp5)
[1] 89.515934 5.755289 9.381499 7.015255 10.470017 9.994823 7.391369
[8] 7.424298 8.807160 8.014210
> rowMax(tmp5)
[1] 469.22207 81.42224 80.38018 81.63478 95.78084 88.40061 89.30328
[8] 86.31748 88.71141 NA
> rowMin(tmp5)
[1] 56.96644 58.08829 52.58092 56.49463 55.01190 55.10450 58.69443 55.53874
[9] 55.95298 NA
>
> colMeans(tmp5)
[1] 117.57285 70.88997 71.01478 70.05532 66.00020 72.05605 68.98571
[8] 68.71573 73.31011 NA 71.87044 71.84411 67.23595 70.33891
[15] 69.35920 69.06970 70.62622 70.00729 71.14182 73.24068
> colSums(tmp5)
[1] 1175.7285 708.8997 710.1478 700.5532 660.0020 720.5605 689.8571
[8] 687.1573 733.1011 NA 718.7044 718.4411 672.3595 703.3891
[15] 693.5920 690.6970 706.2622 700.0729 711.4182 732.4068
> colVars(tmp5)
[1] 15333.63609 63.95686 19.41159 65.74688 55.94613 93.33403
[7] 69.07837 53.52070 162.80355 NA 45.21561 48.72134
[13] 49.37300 87.97596 114.52174 28.50226 62.34270 64.76243
[19] 67.76787 78.03740
> colSd(tmp5)
[1] 123.829060 7.997303 4.405858 8.108445 7.479715 9.660954
[7] 8.311340 7.315785 12.759449 NA 6.724255 6.980067
[13] 7.026592 9.379550 10.701483 5.338751 7.895740 8.047511
[19] 8.232124 8.833878
> colMax(tmp5)
[1] 469.22207 86.94047 77.74338 78.29060 78.79620 95.44749 78.50201
[8] 79.83907 89.30328 NA 80.98352 81.66167 80.23727 81.42224
[15] 87.18237 75.32785 85.20387 80.22414 86.31748 88.71141
> colMin(tmp5)
[1] 67.84968 56.49463 65.15022 57.99942 56.50041 58.79383 55.95298 53.65054
[9] 55.53874 NA 61.77068 59.10162 59.74671 55.01190 56.96644 60.39909
[17] 61.46240 55.01958 58.14643 62.22334
>
> Max(tmp5,na.rm=TRUE)
[1] 469.2221
> Min(tmp5,na.rm=TRUE)
[1] 52.58092
> mean(tmp5,na.rm=TRUE)
[1] 72.53587
> Sum(tmp5,na.rm=TRUE)
[1] 14434.64
> Var(tmp5,na.rm=TRUE)
[1] 868.9541
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.72212 69.14627 67.63177 71.36113 71.87590 72.55954 71.95200 68.82918
[9] 69.19225 72.06499
> rowSums(tmp5,na.rm=TRUE)
[1] 1814.442 1382.925 1352.635 1427.223 1437.518 1451.191 1439.040 1376.584
[9] 1383.845 1369.235
> rowVars(tmp5,na.rm=TRUE)
[1] 8013.10251 33.12335 88.01251 49.21381 109.62125 99.89649
[7] 54.63234 55.12019 77.56607 64.22756
> rowSd(tmp5,na.rm=TRUE)
[1] 89.515934 5.755289 9.381499 7.015255 10.470017 9.994823 7.391369
[8] 7.424298 8.807160 8.014210
> rowMax(tmp5,na.rm=TRUE)
[1] 469.22207 81.42224 80.38018 81.63478 95.78084 88.40061 89.30328
[8] 86.31748 88.71141 85.20387
> rowMin(tmp5,na.rm=TRUE)
[1] 56.96644 58.08829 52.58092 56.49463 55.01190 55.10450 58.69443 55.53874
[9] 55.95298 57.63078
>
> colMeans(tmp5,na.rm=TRUE)
[1] 117.57285 70.88997 71.01478 70.05532 66.00020 72.05605 68.98571
[8] 68.71573 73.31011 66.80973 71.87044 71.84411 67.23595 70.33891
[15] 69.35920 69.06970 70.62622 70.00729 71.14182 73.24068
> colSums(tmp5,na.rm=TRUE)
[1] 1175.7285 708.8997 710.1478 700.5532 660.0020 720.5605 689.8571
[8] 687.1573 733.1011 601.2875 718.7044 718.4411 672.3595 703.3891
[15] 693.5920 690.6970 706.2622 700.0729 711.4182 732.4068
> colVars(tmp5,na.rm=TRUE)
[1] 15333.63609 63.95686 19.41159 65.74688 55.94613 93.33403
[7] 69.07837 53.52070 162.80355 111.15126 45.21561 48.72134
[13] 49.37300 87.97596 114.52174 28.50226 62.34270 64.76243
[19] 67.76787 78.03740
> colSd(tmp5,na.rm=TRUE)
[1] 123.829060 7.997303 4.405858 8.108445 7.479715 9.660954
[7] 8.311340 7.315785 12.759449 10.542830 6.724255 6.980067
[13] 7.026592 9.379550 10.701483 5.338751 7.895740 8.047511
[19] 8.232124 8.833878
> colMax(tmp5,na.rm=TRUE)
[1] 469.22207 86.94047 77.74338 78.29060 78.79620 95.44749 78.50201
[8] 79.83907 89.30328 83.81080 80.98352 81.66167 80.23727 81.42224
[15] 87.18237 75.32785 85.20387 80.22414 86.31748 88.71141
> colMin(tmp5,na.rm=TRUE)
[1] 67.84968 56.49463 65.15022 57.99942 56.50041 58.79383 55.95298 53.65054
[9] 55.53874 52.58092 61.77068 59.10162 59.74671 55.01190 56.96644 60.39909
[17] 61.46240 55.01958 58.14643 62.22334
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.72212 69.14627 67.63177 71.36113 71.87590 72.55954 71.95200 68.82918
[9] 69.19225 NaN
> rowSums(tmp5,na.rm=TRUE)
[1] 1814.442 1382.925 1352.635 1427.223 1437.518 1451.191 1439.040 1376.584
[9] 1383.845 0.000
> rowVars(tmp5,na.rm=TRUE)
[1] 8013.10251 33.12335 88.01251 49.21381 109.62125 99.89649
[7] 54.63234 55.12019 77.56607 NA
> rowSd(tmp5,na.rm=TRUE)
[1] 89.515934 5.755289 9.381499 7.015255 10.470017 9.994823 7.391369
[8] 7.424298 8.807160 NA
> rowMax(tmp5,na.rm=TRUE)
[1] 469.22207 81.42224 80.38018 81.63478 95.78084 88.40061 89.30328
[8] 86.31748 88.71141 NA
> rowMin(tmp5,na.rm=TRUE)
[1] 56.96644 58.08829 52.58092 56.49463 55.01190 55.10450 58.69443 55.53874
[9] 55.95298 NA
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 121.39410 71.14300 71.23694 69.86215 64.57842 72.75090 70.24737
[8] 69.02200 72.08912 NaN 72.99263 70.79599 67.82013 69.79147
[15] 68.82567 69.12858 69.00648 69.47213 71.61449 73.13018
> colSums(tmp5,na.rm=TRUE)
[1] 1092.5469 640.2870 641.1324 628.7593 581.2058 654.7581 632.2263
[8] 621.1980 648.8021 0.0000 656.9337 637.1639 610.3812 628.1232
[15] 619.4310 622.1573 621.0583 625.2491 644.5304 658.1716
> colVars(tmp5,na.rm=TRUE)
[1] 17086.06861 71.23118 21.28282 73.54542 40.19804 99.56912
[7] 59.80559 59.15556 166.38224 NA 36.70017 42.45274
[13] 51.70542 95.60136 125.63458 32.02604 40.62054 69.63577
[19] 73.72539 87.65471
> colSd(tmp5,na.rm=TRUE)
[1] 130.713689 8.439857 4.613331 8.575863 6.340193 9.978433
[7] 7.733408 7.691265 12.898924 NA 6.058066 6.515577
[13] 7.190648 9.777595 11.208683 5.659155 6.373424 8.344805
[19] 8.586349 9.362410
> colMax(tmp5,na.rm=TRUE)
[1] 469.22207 86.94047 77.74338 78.29060 74.66098 95.44749 78.50201
[8] 79.83907 89.30328 -Inf 80.98352 81.66167 80.23727 81.42224
[15] 87.18237 75.32785 79.21198 80.22414 86.31748 88.71141
> colMin(tmp5,na.rm=TRUE)
[1] 67.84968 56.49463 65.15022 57.99942 56.50041 58.79383 55.95298 53.65054
[9] 55.53874 Inf 67.17125 59.10162 59.74671 55.01190 56.96644 60.39909
[17] 61.46240 55.01958 58.14643 62.22334
>
>
>
>
> 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] 222.2478 176.0371 271.5903 292.2299 125.2628 272.9191 348.4339 244.2571
[9] 191.8361 235.7089
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 222.2478 176.0371 271.5903 292.2299 125.2628 272.9191 348.4339 244.2571
[9] 191.8361 235.7089
>
>
>
> 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 -5.684342e-14 0.000000e+00
[6] -1.136868e-13 -5.684342e-14 -1.136868e-13 0.000000e+00 1.705303e-13
[11] 5.684342e-14 -4.263256e-14 -1.705303e-13 -2.273737e-13 -8.526513e-14
[16] -8.526513e-14 -9.947598e-14 8.526513e-14 -5.684342e-14 -1.705303e-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)
+ }
8 15
4 6
1 14
1 4
7 3
10 9
8 14
1 19
2 13
8 19
8 17
3 3
10 14
10 14
5 16
8 20
5 2
10 8
1 6
7 19
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] 3.235552
> Min(tmp)
[1] -2.970902
> mean(tmp)
[1] -0.03909204
> Sum(tmp)
[1] -3.909204
> Var(tmp)
[1] 1.032889
>
> rowMeans(tmp)
[1] -0.03909204
> rowSums(tmp)
[1] -3.909204
> rowVars(tmp)
[1] 1.032889
> rowSd(tmp)
[1] 1.016311
> rowMax(tmp)
[1] 3.235552
> rowMin(tmp)
[1] -2.970902
>
> colMeans(tmp)
[1] -0.076980842 -0.464611164 0.718288233 1.609546669 -0.996194766
[6] 0.830421028 0.669183714 -0.296228223 3.235552382 -0.952010562
[11] -1.503887994 0.904753665 0.794457408 -0.580242892 -0.198718721
[16] 1.774983729 -0.908421271 0.116776901 0.272552411 0.121665718
[21] -0.315664785 -2.970901595 0.896611934 0.905944456 -1.305136179
[26] -0.015003454 -0.207092051 -1.214274694 -0.120187559 0.779149122
[31] -1.398236994 -1.190848589 0.082644244 -0.953048063 1.150961350
[36] 1.367438194 0.790062244 -0.379444783 -0.914588919 -2.802116395
[41] -0.053040832 -0.576024220 -0.586534102 0.917651416 0.460344864
[46] 1.889227772 0.195480609 0.735958443 0.500638583 1.820382278
[51] -0.325935563 0.648878173 0.115965681 0.307062525 -0.219318268
[56] -0.133565337 0.985682565 0.112718364 -0.926460061 -0.626084242
[61] -1.972924550 0.309761614 0.270114392 1.146997614 -0.522125863
[66] 0.298065699 -1.168599816 -1.004038931 0.634028238 -0.790892756
[71] 1.791401959 -1.784025735 0.031438586 0.516542527 -0.060512316
[76] -1.473930701 0.416587078 -0.289127626 -1.033687764 -0.390572097
[81] -0.006761801 -0.171008043 0.075118640 -2.071071470 -1.092287164
[86] 1.395999925 -1.740745578 -0.185260501 0.973234147 0.973712448
[91] -0.024294893 0.313279777 -0.557909478 -0.471947701 0.078976809
[96] -0.082346547 0.658114410 0.522516485 0.471208790 -0.392413460
> colSums(tmp)
[1] -0.076980842 -0.464611164 0.718288233 1.609546669 -0.996194766
[6] 0.830421028 0.669183714 -0.296228223 3.235552382 -0.952010562
[11] -1.503887994 0.904753665 0.794457408 -0.580242892 -0.198718721
[16] 1.774983729 -0.908421271 0.116776901 0.272552411 0.121665718
[21] -0.315664785 -2.970901595 0.896611934 0.905944456 -1.305136179
[26] -0.015003454 -0.207092051 -1.214274694 -0.120187559 0.779149122
[31] -1.398236994 -1.190848589 0.082644244 -0.953048063 1.150961350
[36] 1.367438194 0.790062244 -0.379444783 -0.914588919 -2.802116395
[41] -0.053040832 -0.576024220 -0.586534102 0.917651416 0.460344864
[46] 1.889227772 0.195480609 0.735958443 0.500638583 1.820382278
[51] -0.325935563 0.648878173 0.115965681 0.307062525 -0.219318268
[56] -0.133565337 0.985682565 0.112718364 -0.926460061 -0.626084242
[61] -1.972924550 0.309761614 0.270114392 1.146997614 -0.522125863
[66] 0.298065699 -1.168599816 -1.004038931 0.634028238 -0.790892756
[71] 1.791401959 -1.784025735 0.031438586 0.516542527 -0.060512316
[76] -1.473930701 0.416587078 -0.289127626 -1.033687764 -0.390572097
[81] -0.006761801 -0.171008043 0.075118640 -2.071071470 -1.092287164
[86] 1.395999925 -1.740745578 -0.185260501 0.973234147 0.973712448
[91] -0.024294893 0.313279777 -0.557909478 -0.471947701 0.078976809
[96] -0.082346547 0.658114410 0.522516485 0.471208790 -0.392413460
> 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] -0.076980842 -0.464611164 0.718288233 1.609546669 -0.996194766
[6] 0.830421028 0.669183714 -0.296228223 3.235552382 -0.952010562
[11] -1.503887994 0.904753665 0.794457408 -0.580242892 -0.198718721
[16] 1.774983729 -0.908421271 0.116776901 0.272552411 0.121665718
[21] -0.315664785 -2.970901595 0.896611934 0.905944456 -1.305136179
[26] -0.015003454 -0.207092051 -1.214274694 -0.120187559 0.779149122
[31] -1.398236994 -1.190848589 0.082644244 -0.953048063 1.150961350
[36] 1.367438194 0.790062244 -0.379444783 -0.914588919 -2.802116395
[41] -0.053040832 -0.576024220 -0.586534102 0.917651416 0.460344864
[46] 1.889227772 0.195480609 0.735958443 0.500638583 1.820382278
[51] -0.325935563 0.648878173 0.115965681 0.307062525 -0.219318268
[56] -0.133565337 0.985682565 0.112718364 -0.926460061 -0.626084242
[61] -1.972924550 0.309761614 0.270114392 1.146997614 -0.522125863
[66] 0.298065699 -1.168599816 -1.004038931 0.634028238 -0.790892756
[71] 1.791401959 -1.784025735 0.031438586 0.516542527 -0.060512316
[76] -1.473930701 0.416587078 -0.289127626 -1.033687764 -0.390572097
[81] -0.006761801 -0.171008043 0.075118640 -2.071071470 -1.092287164
[86] 1.395999925 -1.740745578 -0.185260501 0.973234147 0.973712448
[91] -0.024294893 0.313279777 -0.557909478 -0.471947701 0.078976809
[96] -0.082346547 0.658114410 0.522516485 0.471208790 -0.392413460
> colMin(tmp)
[1] -0.076980842 -0.464611164 0.718288233 1.609546669 -0.996194766
[6] 0.830421028 0.669183714 -0.296228223 3.235552382 -0.952010562
[11] -1.503887994 0.904753665 0.794457408 -0.580242892 -0.198718721
[16] 1.774983729 -0.908421271 0.116776901 0.272552411 0.121665718
[21] -0.315664785 -2.970901595 0.896611934 0.905944456 -1.305136179
[26] -0.015003454 -0.207092051 -1.214274694 -0.120187559 0.779149122
[31] -1.398236994 -1.190848589 0.082644244 -0.953048063 1.150961350
[36] 1.367438194 0.790062244 -0.379444783 -0.914588919 -2.802116395
[41] -0.053040832 -0.576024220 -0.586534102 0.917651416 0.460344864
[46] 1.889227772 0.195480609 0.735958443 0.500638583 1.820382278
[51] -0.325935563 0.648878173 0.115965681 0.307062525 -0.219318268
[56] -0.133565337 0.985682565 0.112718364 -0.926460061 -0.626084242
[61] -1.972924550 0.309761614 0.270114392 1.146997614 -0.522125863
[66] 0.298065699 -1.168599816 -1.004038931 0.634028238 -0.790892756
[71] 1.791401959 -1.784025735 0.031438586 0.516542527 -0.060512316
[76] -1.473930701 0.416587078 -0.289127626 -1.033687764 -0.390572097
[81] -0.006761801 -0.171008043 0.075118640 -2.071071470 -1.092287164
[86] 1.395999925 -1.740745578 -0.185260501 0.973234147 0.973712448
[91] -0.024294893 0.313279777 -0.557909478 -0.471947701 0.078976809
[96] -0.082346547 0.658114410 0.522516485 0.471208790 -0.392413460
> colMedians(tmp)
[1] -0.076980842 -0.464611164 0.718288233 1.609546669 -0.996194766
[6] 0.830421028 0.669183714 -0.296228223 3.235552382 -0.952010562
[11] -1.503887994 0.904753665 0.794457408 -0.580242892 -0.198718721
[16] 1.774983729 -0.908421271 0.116776901 0.272552411 0.121665718
[21] -0.315664785 -2.970901595 0.896611934 0.905944456 -1.305136179
[26] -0.015003454 -0.207092051 -1.214274694 -0.120187559 0.779149122
[31] -1.398236994 -1.190848589 0.082644244 -0.953048063 1.150961350
[36] 1.367438194 0.790062244 -0.379444783 -0.914588919 -2.802116395
[41] -0.053040832 -0.576024220 -0.586534102 0.917651416 0.460344864
[46] 1.889227772 0.195480609 0.735958443 0.500638583 1.820382278
[51] -0.325935563 0.648878173 0.115965681 0.307062525 -0.219318268
[56] -0.133565337 0.985682565 0.112718364 -0.926460061 -0.626084242
[61] -1.972924550 0.309761614 0.270114392 1.146997614 -0.522125863
[66] 0.298065699 -1.168599816 -1.004038931 0.634028238 -0.790892756
[71] 1.791401959 -1.784025735 0.031438586 0.516542527 -0.060512316
[76] -1.473930701 0.416587078 -0.289127626 -1.033687764 -0.390572097
[81] -0.006761801 -0.171008043 0.075118640 -2.071071470 -1.092287164
[86] 1.395999925 -1.740745578 -0.185260501 0.973234147 0.973712448
[91] -0.024294893 0.313279777 -0.557909478 -0.471947701 0.078976809
[96] -0.082346547 0.658114410 0.522516485 0.471208790 -0.392413460
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.07698084 -0.4646112 0.7182882 1.609547 -0.9961948 0.830421 0.6691837
[2,] -0.07698084 -0.4646112 0.7182882 1.609547 -0.9961948 0.830421 0.6691837
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -0.2962282 3.235552 -0.9520106 -1.503888 0.9047537 0.7944574 -0.5802429
[2,] -0.2962282 3.235552 -0.9520106 -1.503888 0.9047537 0.7944574 -0.5802429
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -0.1987187 1.774984 -0.9084213 0.1167769 0.2725524 0.1216657 -0.3156648
[2,] -0.1987187 1.774984 -0.9084213 0.1167769 0.2725524 0.1216657 -0.3156648
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -2.970902 0.8966119 0.9059445 -1.305136 -0.01500345 -0.2070921 -1.214275
[2,] -2.970902 0.8966119 0.9059445 -1.305136 -0.01500345 -0.2070921 -1.214275
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] -0.1201876 0.7791491 -1.398237 -1.190849 0.08264424 -0.9530481 1.150961
[2,] -0.1201876 0.7791491 -1.398237 -1.190849 0.08264424 -0.9530481 1.150961
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 1.367438 0.7900622 -0.3794448 -0.9145889 -2.802116 -0.05304083 -0.5760242
[2,] 1.367438 0.7900622 -0.3794448 -0.9145889 -2.802116 -0.05304083 -0.5760242
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.5865341 0.9176514 0.4603449 1.889228 0.1954806 0.7359584 0.5006386
[2,] -0.5865341 0.9176514 0.4603449 1.889228 0.1954806 0.7359584 0.5006386
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 1.820382 -0.3259356 0.6488782 0.1159657 0.3070625 -0.2193183 -0.1335653
[2,] 1.820382 -0.3259356 0.6488782 0.1159657 0.3070625 -0.2193183 -0.1335653
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 0.9856826 0.1127184 -0.9264601 -0.6260842 -1.972925 0.3097616 0.2701144
[2,] 0.9856826 0.1127184 -0.9264601 -0.6260842 -1.972925 0.3097616 0.2701144
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 1.146998 -0.5221259 0.2980657 -1.1686 -1.004039 0.6340282 -0.7908928
[2,] 1.146998 -0.5221259 0.2980657 -1.1686 -1.004039 0.6340282 -0.7908928
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] 1.791402 -1.784026 0.03143859 0.5165425 -0.06051232 -1.473931 0.4165871
[2,] 1.791402 -1.784026 0.03143859 0.5165425 -0.06051232 -1.473931 0.4165871
[,78] [,79] [,80] [,81] [,82] [,83]
[1,] -0.2891276 -1.033688 -0.3905721 -0.006761801 -0.171008 0.07511864
[2,] -0.2891276 -1.033688 -0.3905721 -0.006761801 -0.171008 0.07511864
[,84] [,85] [,86] [,87] [,88] [,89] [,90]
[1,] -2.071071 -1.092287 1.396 -1.740746 -0.1852605 0.9732341 0.9737124
[2,] -2.071071 -1.092287 1.396 -1.740746 -0.1852605 0.9732341 0.9737124
[,91] [,92] [,93] [,94] [,95] [,96]
[1,] -0.02429489 0.3132798 -0.5579095 -0.4719477 0.07897681 -0.08234655
[2,] -0.02429489 0.3132798 -0.5579095 -0.4719477 0.07897681 -0.08234655
[,97] [,98] [,99] [,100]
[1,] 0.6581144 0.5225165 0.4712088 -0.3924135
[2,] 0.6581144 0.5225165 0.4712088 -0.3924135
>
>
> Max(tmp2)
[1] 1.88995
> Min(tmp2)
[1] -3.150902
> mean(tmp2)
[1] -0.0857111
> Sum(tmp2)
[1] -8.57111
> Var(tmp2)
[1] 0.9538535
>
> rowMeans(tmp2)
[1] -0.83448673 0.91566368 -1.66480992 -0.21765874 0.02790386 1.41161465
[7] -0.78426526 0.24151219 0.10636547 1.82307172 -1.17823072 -0.08932670
[13] 1.00828638 0.27082013 -0.61008982 0.63904858 0.46955909 -1.45842488
[19] -0.04790882 1.18682024 0.60378441 -1.09260699 0.26733965 1.46745405
[25] -1.33975748 -0.60444866 0.97157482 -0.82600772 1.27377178 0.63060668
[31] -0.66157850 -0.20830399 -0.70740853 0.68495824 -0.30269659 0.15750081
[37] -0.57232384 -0.71846660 0.49101618 0.65194569 -0.49896775 -1.57293221
[43] -0.06022392 1.57479782 0.39785080 -0.38831296 0.33759762 -0.25366844
[49] -0.95556350 -0.18742115 1.88995001 -3.15090240 0.83382156 0.91455362
[55] -0.44014787 0.85235097 -1.03992336 -2.04314187 0.44072976 -0.85115195
[61] 0.12306619 -0.52845411 -1.39113717 1.15268752 -0.38365961 0.44034107
[67] 0.05789446 0.66528545 0.82618122 -2.76115677 -0.92012166 -0.19976550
[73] 0.06123026 -2.09221931 0.47551355 0.22878765 -0.24069243 -0.49167965
[79] -1.14129032 0.50087860 -0.71926354 -1.05716193 0.89291456 -0.83067935
[85] -0.03235384 1.17531843 0.07448919 -0.39700362 -1.21214704 -1.68388105
[91] 0.99334633 1.32542587 -0.20113273 -0.52596565 1.17843970 -1.09351197
[97] -0.11256228 0.35050073 0.74978678 0.99152907
> rowSums(tmp2)
[1] -0.83448673 0.91566368 -1.66480992 -0.21765874 0.02790386 1.41161465
[7] -0.78426526 0.24151219 0.10636547 1.82307172 -1.17823072 -0.08932670
[13] 1.00828638 0.27082013 -0.61008982 0.63904858 0.46955909 -1.45842488
[19] -0.04790882 1.18682024 0.60378441 -1.09260699 0.26733965 1.46745405
[25] -1.33975748 -0.60444866 0.97157482 -0.82600772 1.27377178 0.63060668
[31] -0.66157850 -0.20830399 -0.70740853 0.68495824 -0.30269659 0.15750081
[37] -0.57232384 -0.71846660 0.49101618 0.65194569 -0.49896775 -1.57293221
[43] -0.06022392 1.57479782 0.39785080 -0.38831296 0.33759762 -0.25366844
[49] -0.95556350 -0.18742115 1.88995001 -3.15090240 0.83382156 0.91455362
[55] -0.44014787 0.85235097 -1.03992336 -2.04314187 0.44072976 -0.85115195
[61] 0.12306619 -0.52845411 -1.39113717 1.15268752 -0.38365961 0.44034107
[67] 0.05789446 0.66528545 0.82618122 -2.76115677 -0.92012166 -0.19976550
[73] 0.06123026 -2.09221931 0.47551355 0.22878765 -0.24069243 -0.49167965
[79] -1.14129032 0.50087860 -0.71926354 -1.05716193 0.89291456 -0.83067935
[85] -0.03235384 1.17531843 0.07448919 -0.39700362 -1.21214704 -1.68388105
[91] 0.99334633 1.32542587 -0.20113273 -0.52596565 1.17843970 -1.09351197
[97] -0.11256228 0.35050073 0.74978678 0.99152907
> 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] -0.83448673 0.91566368 -1.66480992 -0.21765874 0.02790386 1.41161465
[7] -0.78426526 0.24151219 0.10636547 1.82307172 -1.17823072 -0.08932670
[13] 1.00828638 0.27082013 -0.61008982 0.63904858 0.46955909 -1.45842488
[19] -0.04790882 1.18682024 0.60378441 -1.09260699 0.26733965 1.46745405
[25] -1.33975748 -0.60444866 0.97157482 -0.82600772 1.27377178 0.63060668
[31] -0.66157850 -0.20830399 -0.70740853 0.68495824 -0.30269659 0.15750081
[37] -0.57232384 -0.71846660 0.49101618 0.65194569 -0.49896775 -1.57293221
[43] -0.06022392 1.57479782 0.39785080 -0.38831296 0.33759762 -0.25366844
[49] -0.95556350 -0.18742115 1.88995001 -3.15090240 0.83382156 0.91455362
[55] -0.44014787 0.85235097 -1.03992336 -2.04314187 0.44072976 -0.85115195
[61] 0.12306619 -0.52845411 -1.39113717 1.15268752 -0.38365961 0.44034107
[67] 0.05789446 0.66528545 0.82618122 -2.76115677 -0.92012166 -0.19976550
[73] 0.06123026 -2.09221931 0.47551355 0.22878765 -0.24069243 -0.49167965
[79] -1.14129032 0.50087860 -0.71926354 -1.05716193 0.89291456 -0.83067935
[85] -0.03235384 1.17531843 0.07448919 -0.39700362 -1.21214704 -1.68388105
[91] 0.99334633 1.32542587 -0.20113273 -0.52596565 1.17843970 -1.09351197
[97] -0.11256228 0.35050073 0.74978678 0.99152907
> rowMin(tmp2)
[1] -0.83448673 0.91566368 -1.66480992 -0.21765874 0.02790386 1.41161465
[7] -0.78426526 0.24151219 0.10636547 1.82307172 -1.17823072 -0.08932670
[13] 1.00828638 0.27082013 -0.61008982 0.63904858 0.46955909 -1.45842488
[19] -0.04790882 1.18682024 0.60378441 -1.09260699 0.26733965 1.46745405
[25] -1.33975748 -0.60444866 0.97157482 -0.82600772 1.27377178 0.63060668
[31] -0.66157850 -0.20830399 -0.70740853 0.68495824 -0.30269659 0.15750081
[37] -0.57232384 -0.71846660 0.49101618 0.65194569 -0.49896775 -1.57293221
[43] -0.06022392 1.57479782 0.39785080 -0.38831296 0.33759762 -0.25366844
[49] -0.95556350 -0.18742115 1.88995001 -3.15090240 0.83382156 0.91455362
[55] -0.44014787 0.85235097 -1.03992336 -2.04314187 0.44072976 -0.85115195
[61] 0.12306619 -0.52845411 -1.39113717 1.15268752 -0.38365961 0.44034107
[67] 0.05789446 0.66528545 0.82618122 -2.76115677 -0.92012166 -0.19976550
[73] 0.06123026 -2.09221931 0.47551355 0.22878765 -0.24069243 -0.49167965
[79] -1.14129032 0.50087860 -0.71926354 -1.05716193 0.89291456 -0.83067935
[85] -0.03235384 1.17531843 0.07448919 -0.39700362 -1.21214704 -1.68388105
[91] 0.99334633 1.32542587 -0.20113273 -0.52596565 1.17843970 -1.09351197
[97] -0.11256228 0.35050073 0.74978678 0.99152907
>
> colMeans(tmp2)
[1] -0.0857111
> colSums(tmp2)
[1] -8.57111
> colVars(tmp2)
[1] 0.9538535
> colSd(tmp2)
[1] 0.9766543
> colMax(tmp2)
[1] 1.88995
> colMin(tmp2)
[1] -3.150902
> colMedians(tmp2)
[1] -0.05406637
> colRanges(tmp2)
[,1]
[1,] -3.150902
[2,] 1.889950
>
> 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] -3.631865 1.012097 2.815899 2.568570 5.855655 -1.737475 -2.127640
[8] 4.001924 3.923290 -4.772118
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.4722587
[2,] -0.3990457
[3,] -0.3248291
[4,] -0.1820507
[5,] 0.6677033
>
> rowApply(tmp,sum)
[1] -1.6002940 -1.5170646 1.6642959 -1.0015006 -2.8277578 1.3815143
[7] 4.1277063 0.3746199 6.7472372 0.5595815
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 5 5 2 5 6 8 2 1 4 4
[2,] 10 4 6 3 3 5 7 8 6 6
[3,] 9 6 7 6 4 1 5 10 7 9
[4,] 1 9 5 7 9 4 10 3 8 5
[5,] 2 10 4 8 7 9 6 4 10 10
[6,] 8 3 3 4 8 3 4 5 1 3
[7,] 7 2 10 2 2 2 3 6 2 8
[8,] 6 1 8 10 5 6 8 9 9 2
[9,] 3 8 9 9 10 7 1 7 5 1
[10,] 4 7 1 1 1 10 9 2 3 7
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -0.3059826 -0.9045746 1.6559036 2.2518455 2.4238578 0.8440302
[7] -1.7393958 -0.2576498 0.4063029 -2.4627142 -1.9524151 -4.2629148
[13] 4.6754955 0.7540871 2.7277784 -3.1659810 -0.6688080 1.3682752
[19] 0.4634906 0.8802092
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.8737707
[2,] -0.3767631
[3,] -0.1070552
[4,] 0.3882223
[5,] 0.6633841
>
> rowApply(tmp,sum)
[1] -0.61201863 2.12156632 -1.84500557 -0.06092585 3.12722381
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 13 13 11 3 12
[2,] 16 18 4 4 2
[3,] 9 17 6 14 19
[4,] 10 14 12 17 17
[5,] 20 6 18 18 1
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.1070552 0.8865018 -0.3767903 -0.3715900 2.1741767 1.5250690
[2,] 0.6633841 1.1891402 0.8890269 0.6921754 -0.2537416 -0.4553901
[3,] -0.3767631 -1.0988078 -0.5781003 -0.2702621 1.0902931 0.8954262
[4,] -0.8737707 -0.7692697 0.2907877 0.9788031 1.0197121 -0.5079672
[5,] 0.3882223 -1.1121392 1.4309797 1.2227190 -1.6065825 -0.6131077
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.61678200 -1.4802054 0.1609519 -0.2083011 -1.5066485 -0.3893520
[2,] -1.96688977 0.2455619 0.2310848 0.3776557 -0.1908299 -0.9505165
[3,] -0.48595712 1.9955436 -0.4939615 -1.5750094 0.7847516 -1.4118176
[4,] 0.09947056 -0.3077704 1.2520855 -0.3182423 -1.3007163 -1.1811840
[5,] 1.23076255 -0.7107796 -0.7438578 -0.7388172 0.2610280 -0.3300446
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 1.1945288 1.8912378 0.47851718 -0.8258494 -0.7378505 -1.2926700
[2,] 0.7617112 -1.2801747 2.08200157 -2.7436036 0.3155963 -0.1110347
[3,] 1.3001074 -0.4598582 0.01149801 -1.2757955 0.1400045 -0.3955438
[4,] 0.9241322 -0.2997802 -0.29389861 0.8026274 -0.1727552 1.2326724
[5,] 0.4950160 0.9026625 0.44966022 0.8766402 -0.2138031 1.9348513
[,19] [,20]
[1,] -0.6496600 -0.36024727
[2,] 1.8465377 0.77987132
[3,] -0.5863899 0.94563645
[4,] -0.1268904 -0.50897184
[5,] -0.0201067 0.02392056
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/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: /home/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: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 562 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /home/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 1.420297 -1.454637 0.2505494 2.056709 -1.134728 0.4497942 0.6362926
col8 col9 col10 col11 col12 col13 col14
row1 0.2605102 0.6837089 -0.9394761 -1.213741 -1.304571 -0.05550012 -0.5364633
col15 col16 col17 col18 col19 col20
row1 0.3573758 0.0731427 -0.1486669 0.7950203 0.3610057 1.060476
> tmp[,"col10"]
col10
row1 -0.93947610
row2 -0.21962265
row3 0.42850558
row4 -0.02913451
row5 -0.34839531
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 1.4202973 -1.454637 0.2505494 2.0567088 -1.134728 0.44979425 0.6362926
row5 -0.3535142 1.754144 -0.1353420 0.1915787 -1.361334 -0.09260783 -0.1115134
col8 col9 col10 col11 col12 col13
row1 0.2605102 0.6837089 -0.9394761 -1.2137414 -1.3045713 -0.05550012
row5 0.1934171 0.8761254 -0.3483953 0.1075734 -0.4185848 0.13976557
col14 col15 col16 col17 col18 col19 col20
row1 -0.5364633 0.3573758 0.0731427 -0.1486669 0.7950203 0.3610057 1.0604759
row5 -0.8259343 0.5614879 -1.3909244 -0.3079950 1.1560415 -0.2584090 -0.1555821
> tmp[,c("col6","col20")]
col6 col20
row1 0.44979425 1.0604759
row2 -0.25644308 0.3464806
row3 -0.96387868 0.3948869
row4 -0.08368628 -1.0851416
row5 -0.09260783 -0.1555821
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.44979425 1.0604759
row5 -0.09260783 -0.1555821
>
>
>
>
> 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 47.30094 49.08175 50.68085 49.79916 50.18136 106.1017 48.76627 49.56101
col9 col10 col11 col12 col13 col14 col15 col16
row1 47.67481 50.56933 50.67054 50.57776 47.94137 49.74372 51.47827 49.52828
col17 col18 col19 col20
row1 50.58477 50.93946 50.0073 106.9914
> tmp[,"col10"]
col10
row1 50.56933
row2 28.52841
row3 29.01175
row4 31.10135
row5 50.23113
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 47.30094 49.08175 50.68085 49.79916 50.18136 106.1017 48.76627 49.56101
row5 49.69529 50.09614 49.96560 50.54597 50.15982 104.2796 48.57901 52.39217
col9 col10 col11 col12 col13 col14 col15 col16
row1 47.67481 50.56933 50.67054 50.57776 47.94137 49.74372 51.47827 49.52828
row5 49.32793 50.23113 49.08302 49.13453 50.95901 51.26230 50.19428 51.59825
col17 col18 col19 col20
row1 50.58477 50.93946 50.0073 106.9914
row5 48.61187 51.05072 49.6331 105.2855
> tmp[,c("col6","col20")]
col6 col20
row1 106.10174 106.99139
row2 74.29468 75.00303
row3 74.41003 74.04033
row4 74.79120 75.05705
row5 104.27956 105.28546
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 106.1017 106.9914
row5 104.2796 105.2855
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 106.1017 106.9914
row5 104.2796 105.2855
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -0.31277096
[2,] -0.60840886
[3,] -0.61014765
[4,] 0.96395231
[5,] -0.03567421
> tmp[,c("col17","col7")]
col17 col7
[1,] 1.44946942 0.2840467
[2,] 0.52206974 1.3729454
[3,] -0.34940055 0.9576918
[4,] -0.22157556 0.7638360
[5,] -0.06796738 -0.0613374
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -1.1478844 -0.6387328
[2,] -0.1557958 -0.7818024
[3,] -0.3050748 -0.5417928
[4,] 1.7595891 0.5735580
[5,] -0.3563553 1.3813067
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -1.147884
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -1.1478844
[2,] -0.1557958
>
>
>
> 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 -1.1573944 0.50531787 0.7178785 -0.7603119 0.9320929 0.05271228
row1 -0.2737809 -0.03204562 -0.1042524 1.9277869 1.1252167 0.48816747
[,7] [,8] [,9] [,10] [,11] [,12] [,13]
row3 -1.8183224 -1.1828470 0.2930819 -0.973566 0.9771475 0.8639404 0.4054529
row1 0.7573451 -0.1181162 -0.6333097 1.364831 -0.7575110 0.8023731 -1.7863823
[,14] [,15] [,16] [,17] [,18] [,19]
row3 -1.17659175 -0.4750582 0.8637401 1.636131 -0.4678707 -0.1868623
row1 0.06580568 -0.7699538 -0.5561966 -1.519826 0.8593742 -0.4799610
[,20]
row3 0.4906457
row1 -1.6572350
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.338096 -0.3374274 0.8680515 2.309414 1.249961 -0.7432701 0.4045369
[,8] [,9] [,10]
row2 1.145144 -1.119174 -0.4278526
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -0.5088789 -0.6064676 -0.06080714 -1.716359 0.1410151 0.1443671 1.236971
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.818311 -0.1138502 0.6528139 -0.3620912 -0.5925152 1.89195 -0.08111299
[,15] [,16] [,17] [,18] [,19] [,20]
row5 0.4173214 -1.626399 -0.4742676 1.253008 1.293882 0.7513808
>
>
> 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: 0xfa29aa0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2c09b2f62609"
[2] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2c09b3485ca4f"
[3] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2c09b25534d74"
[4] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2c09b63af4093"
[5] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2c09b3269a02f"
[6] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2c09b4b555d12"
[7] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2c09b6804652f"
[8] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2c09b13aac4fe"
[9] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2c09b747b5c65"
[10] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2c09b70c01905"
[11] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2c09b24327417"
[12] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2c09b16700b76"
[13] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2c09b519114d7"
[14] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2c09b8b96854"
[15] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2c09b418005ea"
>
>
> ### 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: 0x10efea00>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x10efea00>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x10efea00>
> rowMedians(tmp)
[1] -0.122232492 0.098914939 -0.375754318 -0.216368780 0.268054979
[6] 0.594346164 -0.214419860 0.128983473 -0.248551693 0.375428799
[11] 0.350262567 -0.068772670 0.258302701 -0.058708110 -0.229437450
[16] -0.058844435 0.339089883 -0.195374891 0.081046805 -0.040206283
[21] -0.008534181 -0.421582622 0.576967999 -0.604073964 0.135006709
[26] 0.158008445 0.057445481 -1.096531843 -0.328461930 0.170833786
[31] 0.175134012 -0.504363945 0.610338387 -0.327236543 0.299335426
[36] -0.104857370 0.021550218 0.937205403 -0.059236441 0.237068430
[41] 0.300181231 -0.216658584 -0.217056905 -0.516549446 -0.365012950
[46] 0.031737285 0.053369469 -0.474240491 0.078721579 -0.429983449
[51] 0.502108854 -0.333175732 -0.178229159 -0.399185165 0.231270899
[56] -0.062942445 0.109966696 -0.274217255 -0.584112535 0.764429630
[61] -1.013009547 -0.167482397 0.012506691 -0.477316906 -0.830513337
[66] 0.441917415 0.164743311 -0.139099279 0.312109618 0.083169953
[71] 0.340150261 0.088249870 0.522014662 0.306713637 0.091586457
[76] -0.302315862 0.572092690 -0.172062740 -0.526162842 -0.041372259
[81] -0.217270860 -0.306676022 -0.013464694 0.310203889 -0.383854479
[86] -0.175484969 0.100287871 0.124754551 -0.170571560 -0.054436201
[91] 0.038524453 0.103584527 -0.191159830 -0.314591310 0.182111129
[96] -0.597589197 -0.530853706 0.149745721 -0.125255270 -0.127831590
[101] -0.397799297 0.197468569 -0.327116653 0.227688730 -0.276217702
[106] 0.192929245 -0.035303967 0.404098566 0.153890892 -0.007657003
[111] -0.578079508 -0.237581721 0.258961584 0.199513627 -0.202230484
[116] 0.678608875 -0.346279421 -0.235414241 0.271453314 -0.102223049
[121] -0.567199489 0.193892924 -0.151054227 -0.135910956 -0.108586074
[126] 0.116485748 -0.040705170 0.090028733 0.125580296 -0.705650637
[131] 0.246270446 0.366499662 0.017894962 -0.096762263 -0.368002152
[136] 0.167459568 0.075658638 0.315378917 0.186338404 0.129510890
[141] 0.175567517 -0.100068373 0.229476904 -0.200824386 -0.361869199
[146] 0.335922281 0.132306204 -0.174665546 0.128451866 -0.097465811
[151] 0.197649637 0.083394731 -0.208095366 -0.197525286 -0.347372709
[156] -0.626913710 0.248532913 0.311700757 0.065628899 0.095402636
[161] -0.326191056 0.119460064 -0.099629821 -0.096640260 0.380324149
[166] 0.202700752 -0.418691749 -0.290151770 0.107369133 0.009029441
[171] 0.020794956 0.509252779 0.036298261 0.244183623 -0.088325523
[176] -0.039588351 -0.204652761 -0.202054313 0.205601341 -0.296880497
[181] -0.080485068 0.248694290 0.058191689 -0.546876742 -0.754307128
[186] 0.204755675 -0.959039516 -0.200460980 0.100810287 0.165268412
[191] -0.094578878 -0.288389152 0.249558536 0.057779622 0.458200037
[196] -0.291910973 -0.241019706 0.239092154 -0.442290558 -0.242962749
[201] 0.158532994 0.159319788 0.322410099 0.322480822 -0.824750538
[206] 0.189552410 0.427020071 -0.368501660 0.013642137 -0.004196458
[211] -0.284852268 0.163119402 -0.189922086 0.294367975 -0.559511748
[216] 0.088631590 -0.239220897 0.220441177 -0.235239656 0.113043253
[221] 0.277957022 0.426121490 -0.292198859 -0.281545575 0.063852587
[226] -0.066787443 -0.173210542 0.297117903 0.235066351 0.406158676
>
> proc.time()
user system elapsed
1.879 0.842 2.747
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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: 0x30482ff0>
> .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: 0x30482ff0>
> .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: 0x30482ff0>
> .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: 0x30482ff0>
> 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: 0x303680e0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x303680e0>
> .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: 0x303680e0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x303680e0>
> .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: 0x303680e0>
> 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: 0x2f2ef520>
> .Call("R_bm_AddColumn",P)
<pointer: 0x2f2ef520>
> .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: 0x2f2ef520>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x2f2ef520>
> .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: 0x2f2ef520>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x2f2ef520>
> .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: 0x2f2ef520>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x2f2ef520>
> .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: 0x2f2ef520>
> 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: 0x2ecf3720>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x2ecf3720>
> .Call("R_bm_AddColumn",P)
<pointer: 0x2ecf3720>
> .Call("R_bm_AddColumn",P)
<pointer: 0x2ecf3720>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile2c28936baeed7" "BufferedMatrixFile2c28942233c68"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile2c28936baeed7" "BufferedMatrixFile2c28942233c68"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x2fbe37d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x2fbe37d0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x2fbe37d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x2fbe37d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x2fbe37d0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x2fbe37d0>
> .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: 0x2fceac90>
> .Call("R_bm_AddColumn",P)
<pointer: 0x2fceac90>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x2fceac90>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x2fceac90>
> 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: 0x30f93110>
> .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: 0x30f93110>
> rm(P)
>
> proc.time()
user system elapsed
0.329 0.038 0.352
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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
0.329 0.039 0.352