Ben Bolstad
| Snapshot Date: 2026-05-25 13:40 -0400 (Mon, 25 May 2026) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: RELEASE_3_23 |
| git_last_commit: 9d72964 |
| git_last_commit_date: 2026-04-28 08:32:08 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-26 11:32 -0400 (Tue, 26 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4995 |
| 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 262/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.76.0 (landing page) Ben Bolstad
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for BufferedMatrix in R Universe. | ||||||||||||||
|
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: 1.76.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BufferedMatrix_1.76.0.tar.gz |
| StartedAt: 2026-05-25 22:07:36 -0400 (Mon, 25 May 2026) |
| EndedAt: 2026-05-25 22:08:01 -0400 (Mon, 25 May 2026) |
| EllapsedTime: 25.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BufferedMatrix_1.76.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-26 02:07:36 UTC
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.76.0’
* 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: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* 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 ... INFO
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ...* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.76.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/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){
| ^~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c init_package.c -o init_package.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/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 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-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
0.260 0.032 0.283
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-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-3.23-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 480233 25.7 1053308 56.3 637571 34.1
Vcells 887253 6.8 8388608 64.0 2083896 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] "Mon May 25 22:07:52 2026"
> 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] "Mon May 25 22:07:52 2026"
>
>
> 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: 0x5816aa081690>
>
>
>
> 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] "Mon May 25 22:07:52 2026"
> 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] "Mon May 25 22:07:53 2026"
>
> ColMode(tmp2)
<pointer: 0x5816aa081690>
>
>
>
> ### 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,] 101.0100929 -0.48337166 -0.5670537 -0.3692696
[2,] -0.3711654 -0.21867160 -0.6807460 -0.4879294
[3,] 0.4996616 0.12233690 -0.4258464 -1.8825596
[4,] 0.8517514 -0.01286822 -1.9877705 -1.2868381
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-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,] 101.0100929 0.48337166 0.5670537 0.3692696
[2,] 0.3711654 0.21867160 0.6807460 0.4879294
[3,] 0.4996616 0.12233690 0.4258464 1.8825596
[4,] 0.8517514 0.01286822 1.9877705 1.2868381
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-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,] 10.0503778 0.6952493 0.7530297 0.6076755
[2,] 0.6092335 0.4676233 0.8250733 0.6985195
[3,] 0.7068674 0.3497669 0.6525691 1.3720640
[4,] 0.9229038 0.1134382 1.4098832 1.1343889
>
> 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-3.23-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,] 226.51387 32.43587 33.09735 31.44602
[2,] 31.46350 29.89491 33.93148 32.47312
[3,] 32.56834 28.62001 31.95154 40.60320
[4,] 35.08079 26.14725 41.08660 37.63073
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x5816ab4350c0>
> exp(tmp5)
<pointer: 0x5816ab4350c0>
> log(tmp5,2)
<pointer: 0x5816ab4350c0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 471.4589
> Min(tmp5)
[1] 53.42922
> mean(tmp5)
[1] 73.63149
> Sum(tmp5)
[1] 14726.3
> Var(tmp5)
[1] 861.6986
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 94.66710 69.44817 71.25975 69.93805 74.47360 70.54674 71.60224 71.09891
[9] 73.53288 69.74745
> rowSums(tmp5)
[1] 1893.342 1388.963 1425.195 1398.761 1489.472 1410.935 1432.045 1421.978
[9] 1470.658 1394.949
> rowVars(tmp5)
[1] 7900.81719 43.83450 63.50688 71.65429 87.47725 47.66134
[7] 69.38666 62.24471 82.49073 53.85850
> rowSd(tmp5)
[1] 88.886541 6.620763 7.969120 8.464885 9.352928 6.903719 8.329866
[8] 7.889531 9.082441 7.338835
> rowMax(tmp5)
[1] 471.45894 79.69637 86.26080 85.51638 94.82502 85.99702 84.40761
[8] 86.03586 90.69704 82.29858
> rowMin(tmp5)
[1] 63.13828 57.68539 55.97209 54.42207 58.83759 59.28632 53.42922 58.13448
[9] 57.50979 58.38122
>
> colMeans(tmp5)
[1] 110.44369 70.37367 71.74004 76.67932 71.80493 66.25901 68.62152
[8] 69.65073 73.95173 67.49087 76.36686 74.03177 72.64197 76.06023
[15] 73.15343 69.82111 67.82849 77.73744 69.83956 68.13340
> colSums(tmp5)
[1] 1104.4369 703.7367 717.4004 766.7932 718.0493 662.5901 686.2152
[8] 696.5073 739.5173 674.9087 763.6686 740.3177 726.4197 760.6023
[15] 731.5343 698.2111 678.2849 777.3744 698.3956 681.3340
> colVars(tmp5)
[1] 16150.23122 110.64717 36.70513 86.65566 42.08010 66.35135
[7] 44.17402 67.18417 106.24079 60.35196 39.42533 26.60860
[13] 84.07220 17.30645 57.70144 49.21970 65.27209 36.06609
[19] 44.34648 40.83653
> colSd(tmp5)
[1] 127.083560 10.518896 6.058476 9.308902 6.486918 8.145634
[7] 6.646354 8.196595 10.307317 7.768652 6.278960 5.158352
[13] 9.169090 4.160102 7.596146 7.015675 8.079114 6.005505
[19] 6.659316 6.390347
> colMax(tmp5)
[1] 471.45894 86.30713 85.51638 94.82502 82.29858 78.86992 79.60766
[8] 82.83004 90.69704 86.26080 82.84716 84.23101 86.44557 82.45938
[15] 80.23573 82.64304 80.83466 86.03586 81.62059 78.74462
> colMin(tmp5)
[1] 58.13448 54.42207 66.22940 65.45078 60.34073 53.42922 57.50979 58.66320
[9] 58.83759 59.08575 60.82322 69.07830 59.87416 69.52195 59.28632 59.75772
[17] 55.56812 68.42292 59.48617 57.68539
>
>
> ### 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] 94.66710 69.44817 71.25975 69.93805 74.47360 70.54674 71.60224 NA
[9] 73.53288 69.74745
> rowSums(tmp5)
[1] 1893.342 1388.963 1425.195 1398.761 1489.472 1410.935 1432.045 NA
[9] 1470.658 1394.949
> rowVars(tmp5)
[1] 7900.81719 43.83450 63.50688 71.65429 87.47725 47.66134
[7] 69.38666 65.69943 82.49073 53.85850
> rowSd(tmp5)
[1] 88.886541 6.620763 7.969120 8.464885 9.352928 6.903719 8.329866
[8] 8.105519 9.082441 7.338835
> rowMax(tmp5)
[1] 471.45894 79.69637 86.26080 85.51638 94.82502 85.99702 84.40761
[8] NA 90.69704 82.29858
> rowMin(tmp5)
[1] 63.13828 57.68539 55.97209 54.42207 58.83759 59.28632 53.42922 NA
[9] 57.50979 58.38122
>
> colMeans(tmp5)
[1] 110.44369 70.37367 71.74004 NA 71.80493 66.25901 68.62152
[8] 69.65073 73.95173 67.49087 76.36686 74.03177 72.64197 76.06023
[15] 73.15343 69.82111 67.82849 77.73744 69.83956 68.13340
> colSums(tmp5)
[1] 1104.4369 703.7367 717.4004 NA 718.0493 662.5901 686.2152
[8] 696.5073 739.5173 674.9087 763.6686 740.3177 726.4197 760.6023
[15] 731.5343 698.2111 678.2849 777.3744 698.3956 681.3340
> colVars(tmp5)
[1] 16150.23122 110.64717 36.70513 NA 42.08010 66.35135
[7] 44.17402 67.18417 106.24079 60.35196 39.42533 26.60860
[13] 84.07220 17.30645 57.70144 49.21970 65.27209 36.06609
[19] 44.34648 40.83653
> colSd(tmp5)
[1] 127.083560 10.518896 6.058476 NA 6.486918 8.145634
[7] 6.646354 8.196595 10.307317 7.768652 6.278960 5.158352
[13] 9.169090 4.160102 7.596146 7.015675 8.079114 6.005505
[19] 6.659316 6.390347
> colMax(tmp5)
[1] 471.45894 86.30713 85.51638 NA 82.29858 78.86992 79.60766
[8] 82.83004 90.69704 86.26080 82.84716 84.23101 86.44557 82.45938
[15] 80.23573 82.64304 80.83466 86.03586 81.62059 78.74462
> colMin(tmp5)
[1] 58.13448 54.42207 66.22940 NA 60.34073 53.42922 57.50979 58.66320
[9] 58.83759 59.08575 60.82322 69.07830 59.87416 69.52195 59.28632 59.75772
[17] 55.56812 68.42292 59.48617 57.68539
>
> Max(tmp5,na.rm=TRUE)
[1] 471.4589
> Min(tmp5,na.rm=TRUE)
[1] 53.42922
> mean(tmp5,na.rm=TRUE)
[1] 73.64302
> Sum(tmp5,na.rm=TRUE)
[1] 14654.96
> Var(tmp5,na.rm=TRUE)
[1] 866.0239
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 94.66710 69.44817 71.25975 69.93805 74.47360 70.54674 71.60224 71.08638
[9] 73.53288 69.74745
> rowSums(tmp5,na.rm=TRUE)
[1] 1893.342 1388.963 1425.195 1398.761 1489.472 1410.935 1432.045 1350.641
[9] 1470.658 1394.949
> rowVars(tmp5,na.rm=TRUE)
[1] 7900.81719 43.83450 63.50688 71.65429 87.47725 47.66134
[7] 69.38666 65.69943 82.49073 53.85850
> rowSd(tmp5,na.rm=TRUE)
[1] 88.886541 6.620763 7.969120 8.464885 9.352928 6.903719 8.329866
[8] 8.105519 9.082441 7.338835
> rowMax(tmp5,na.rm=TRUE)
[1] 471.45894 79.69637 86.26080 85.51638 94.82502 85.99702 84.40761
[8] 86.03586 90.69704 82.29858
> rowMin(tmp5,na.rm=TRUE)
[1] 63.13828 57.68539 55.97209 54.42207 58.83759 59.28632 53.42922 58.13448
[9] 57.50979 58.38122
>
> colMeans(tmp5,na.rm=TRUE)
[1] 110.44369 70.37367 71.74004 77.27291 71.80493 66.25901 68.62152
[8] 69.65073 73.95173 67.49087 76.36686 74.03177 72.64197 76.06023
[15] 73.15343 69.82111 67.82849 77.73744 69.83956 68.13340
> colSums(tmp5,na.rm=TRUE)
[1] 1104.4369 703.7367 717.4004 695.4562 718.0493 662.5901 686.2152
[8] 696.5073 739.5173 674.9087 763.6686 740.3177 726.4197 760.6023
[15] 731.5343 698.2111 678.2849 777.3744 698.3956 681.3340
> colVars(tmp5,na.rm=TRUE)
[1] 16150.23122 110.64717 36.70513 93.52363 42.08010 66.35135
[7] 44.17402 67.18417 106.24079 60.35196 39.42533 26.60860
[13] 84.07220 17.30645 57.70144 49.21970 65.27209 36.06609
[19] 44.34648 40.83653
> colSd(tmp5,na.rm=TRUE)
[1] 127.083560 10.518896 6.058476 9.670762 6.486918 8.145634
[7] 6.646354 8.196595 10.307317 7.768652 6.278960 5.158352
[13] 9.169090 4.160102 7.596146 7.015675 8.079114 6.005505
[19] 6.659316 6.390347
> colMax(tmp5,na.rm=TRUE)
[1] 471.45894 86.30713 85.51638 94.82502 82.29858 78.86992 79.60766
[8] 82.83004 90.69704 86.26080 82.84716 84.23101 86.44557 82.45938
[15] 80.23573 82.64304 80.83466 86.03586 81.62059 78.74462
> colMin(tmp5,na.rm=TRUE)
[1] 58.13448 54.42207 66.22940 65.45078 60.34073 53.42922 57.50979 58.66320
[9] 58.83759 59.08575 60.82322 69.07830 59.87416 69.52195 59.28632 59.75772
[17] 55.56812 68.42292 59.48617 57.68539
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 94.66710 69.44817 71.25975 69.93805 74.47360 70.54674 71.60224 NaN
[9] 73.53288 69.74745
> rowSums(tmp5,na.rm=TRUE)
[1] 1893.342 1388.963 1425.195 1398.761 1489.472 1410.935 1432.045 0.000
[9] 1470.658 1394.949
> rowVars(tmp5,na.rm=TRUE)
[1] 7900.81719 43.83450 63.50688 71.65429 87.47725 47.66134
[7] 69.38666 NA 82.49073 53.85850
> rowSd(tmp5,na.rm=TRUE)
[1] 88.886541 6.620763 7.969120 8.464885 9.352928 6.903719 8.329866
[8] NA 9.082441 7.338835
> rowMax(tmp5,na.rm=TRUE)
[1] 471.45894 79.69637 86.26080 85.51638 94.82502 85.99702 84.40761
[8] NA 90.69704 82.29858
> rowMin(tmp5,na.rm=TRUE)
[1] 63.13828 57.68539 55.97209 54.42207 58.83759 59.28632 53.42922 NA
[9] 57.50979 58.38122
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 116.25582 69.49719 72.07057 NaN 71.84055 66.76986 68.09028
[8] 70.87156 74.40202 67.59468 75.94487 73.62170 71.90265 76.22650
[15] 72.36651 70.32620 67.35039 76.81540 70.98994 68.04814
> colSums(tmp5,na.rm=TRUE)
[1] 1046.3024 625.4747 648.6351 0.0000 646.5649 600.9287 612.8125
[8] 637.8441 669.6182 608.3522 683.5038 662.5953 647.1239 686.0385
[15] 651.2986 632.9358 606.1535 691.3386 638.9094 612.4333
> colVars(tmp5,na.rm=TRUE)
[1] 17788.97496 115.83560 40.06424 NA 47.32584 71.70936
[7] 46.52085 58.81472 117.23981 67.77470 42.35015 28.04284
[13] 88.43215 19.15876 57.94760 52.50213 70.85953 31.00995
[19] 35.00193 45.85932
> colSd(tmp5,na.rm=TRUE)
[1] 133.375316 10.762695 6.329632 NA 6.879378 8.468138
[7] 6.820619 7.669076 10.827733 8.232539 6.507700 5.295549
[13] 9.403837 4.377072 7.612332 7.245835 8.417810 5.568658
[19] 5.916243 6.771951
> colMax(tmp5,na.rm=TRUE)
[1] 471.45894 86.30713 85.51638 -Inf 82.29858 78.86992 79.60766
[8] 82.83004 90.69704 86.26080 82.84716 84.23101 86.44557 82.45938
[15] 79.85169 82.64304 80.83466 84.77797 81.62059 78.74462
> colMin(tmp5,na.rm=TRUE)
[1] 60.00308 54.42207 66.22940 Inf 60.34073 53.42922 57.50979 59.52086
[9] 58.83759 59.08575 60.82322 69.07830 59.87416 69.52195 59.28632 59.75772
[17] 55.56812 68.42292 63.13828 57.68539
>
>
>
>
> 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] 311.7204 268.4406 222.9136 192.5925 151.8502 129.6303 287.9043 169.5808
[9] 188.8083 186.7212
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 311.7204 268.4406 222.9136 192.5925 151.8502 129.6303 287.9043 169.5808
[9] 188.8083 186.7212
>
>
>
> 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 1.421085e-14 1.136868e-13 -5.684342e-14 -5.684342e-14
[6] 2.842171e-13 4.263256e-14 -1.136868e-13 -5.684342e-14 0.000000e+00
[11] -8.526513e-14 8.526513e-14 -2.842171e-14 1.705303e-13 -2.273737e-13
[16] -5.684342e-14 2.557954e-13 -3.410605e-13 1.989520e-13 0.000000e+00
>
>
>
>
>
>
>
>
>
>
> ## 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)
+ }
7 14
2 11
4 2
10 9
4 17
6 6
8 17
1 4
6 16
6 20
1 1
8 1
9 9
7 7
9 20
2 13
2 15
9 15
7 20
6 15
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] 3.189976
> Min(tmp)
[1] -2.196979
> mean(tmp)
[1] 0.2586959
> Sum(tmp)
[1] 25.86959
> Var(tmp)
[1] 0.9886535
>
> rowMeans(tmp)
[1] 0.2586959
> rowSums(tmp)
[1] 25.86959
> rowVars(tmp)
[1] 0.9886535
> rowSd(tmp)
[1] 0.9943106
> rowMax(tmp)
[1] 3.189976
> rowMin(tmp)
[1] -2.196979
>
> colMeans(tmp)
[1] -0.029569253 -0.455893959 -0.912238300 2.030428553 1.224819981
[6] 0.625973391 -0.493234012 0.201082653 1.575461399 -0.375206173
[11] -0.623138120 0.154108909 0.365052760 -1.032278860 -1.347545787
[16] 3.189975846 -1.138193312 0.986702383 -2.196979489 0.355505743
[21] 1.716610508 -0.527850024 -0.147098747 0.512935731 -0.771844977
[26] 0.718883603 0.452948050 1.659936994 0.934143415 0.562965691
[31] 1.061297862 0.583404359 -1.330257806 -0.903246104 0.545889966
[36] 0.671288399 1.595755976 0.376760919 -1.643041130 0.963625247
[41] 1.655336026 -0.960297797 0.668094860 -0.320270708 0.635927325
[46] 0.314866348 -0.396259982 0.264557477 -1.074885909 0.174385353
[51] 0.055591941 1.288138677 0.794117417 0.869098487 -0.470878788
[56] -0.270979002 0.249125854 0.236288970 0.494885010 0.746430323
[61] -1.375718452 0.702513001 0.961848988 0.008218281 0.846459448
[66] 0.570249601 1.206156350 0.539742743 -0.035273770 -0.221343121
[71] 2.064022223 -0.223729411 0.385658425 0.334225746 -0.573454095
[76] 1.745283146 1.234005193 1.047301603 0.039672661 2.014898039
[81] -1.943840541 -0.662198182 -0.015978531 -0.523450004 -1.285554926
[86] 1.044646520 1.485137045 0.506525990 -1.719657900 1.374694331
[91] 0.575192025 -0.043405404 -2.013608685 0.564385727 0.568201853
[96] 1.204391013 -0.540394201 0.850014494 0.316852466 0.765689295
> colSums(tmp)
[1] -0.029569253 -0.455893959 -0.912238300 2.030428553 1.224819981
[6] 0.625973391 -0.493234012 0.201082653 1.575461399 -0.375206173
[11] -0.623138120 0.154108909 0.365052760 -1.032278860 -1.347545787
[16] 3.189975846 -1.138193312 0.986702383 -2.196979489 0.355505743
[21] 1.716610508 -0.527850024 -0.147098747 0.512935731 -0.771844977
[26] 0.718883603 0.452948050 1.659936994 0.934143415 0.562965691
[31] 1.061297862 0.583404359 -1.330257806 -0.903246104 0.545889966
[36] 0.671288399 1.595755976 0.376760919 -1.643041130 0.963625247
[41] 1.655336026 -0.960297797 0.668094860 -0.320270708 0.635927325
[46] 0.314866348 -0.396259982 0.264557477 -1.074885909 0.174385353
[51] 0.055591941 1.288138677 0.794117417 0.869098487 -0.470878788
[56] -0.270979002 0.249125854 0.236288970 0.494885010 0.746430323
[61] -1.375718452 0.702513001 0.961848988 0.008218281 0.846459448
[66] 0.570249601 1.206156350 0.539742743 -0.035273770 -0.221343121
[71] 2.064022223 -0.223729411 0.385658425 0.334225746 -0.573454095
[76] 1.745283146 1.234005193 1.047301603 0.039672661 2.014898039
[81] -1.943840541 -0.662198182 -0.015978531 -0.523450004 -1.285554926
[86] 1.044646520 1.485137045 0.506525990 -1.719657900 1.374694331
[91] 0.575192025 -0.043405404 -2.013608685 0.564385727 0.568201853
[96] 1.204391013 -0.540394201 0.850014494 0.316852466 0.765689295
> 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] -0.029569253 -0.455893959 -0.912238300 2.030428553 1.224819981
[6] 0.625973391 -0.493234012 0.201082653 1.575461399 -0.375206173
[11] -0.623138120 0.154108909 0.365052760 -1.032278860 -1.347545787
[16] 3.189975846 -1.138193312 0.986702383 -2.196979489 0.355505743
[21] 1.716610508 -0.527850024 -0.147098747 0.512935731 -0.771844977
[26] 0.718883603 0.452948050 1.659936994 0.934143415 0.562965691
[31] 1.061297862 0.583404359 -1.330257806 -0.903246104 0.545889966
[36] 0.671288399 1.595755976 0.376760919 -1.643041130 0.963625247
[41] 1.655336026 -0.960297797 0.668094860 -0.320270708 0.635927325
[46] 0.314866348 -0.396259982 0.264557477 -1.074885909 0.174385353
[51] 0.055591941 1.288138677 0.794117417 0.869098487 -0.470878788
[56] -0.270979002 0.249125854 0.236288970 0.494885010 0.746430323
[61] -1.375718452 0.702513001 0.961848988 0.008218281 0.846459448
[66] 0.570249601 1.206156350 0.539742743 -0.035273770 -0.221343121
[71] 2.064022223 -0.223729411 0.385658425 0.334225746 -0.573454095
[76] 1.745283146 1.234005193 1.047301603 0.039672661 2.014898039
[81] -1.943840541 -0.662198182 -0.015978531 -0.523450004 -1.285554926
[86] 1.044646520 1.485137045 0.506525990 -1.719657900 1.374694331
[91] 0.575192025 -0.043405404 -2.013608685 0.564385727 0.568201853
[96] 1.204391013 -0.540394201 0.850014494 0.316852466 0.765689295
> colMin(tmp)
[1] -0.029569253 -0.455893959 -0.912238300 2.030428553 1.224819981
[6] 0.625973391 -0.493234012 0.201082653 1.575461399 -0.375206173
[11] -0.623138120 0.154108909 0.365052760 -1.032278860 -1.347545787
[16] 3.189975846 -1.138193312 0.986702383 -2.196979489 0.355505743
[21] 1.716610508 -0.527850024 -0.147098747 0.512935731 -0.771844977
[26] 0.718883603 0.452948050 1.659936994 0.934143415 0.562965691
[31] 1.061297862 0.583404359 -1.330257806 -0.903246104 0.545889966
[36] 0.671288399 1.595755976 0.376760919 -1.643041130 0.963625247
[41] 1.655336026 -0.960297797 0.668094860 -0.320270708 0.635927325
[46] 0.314866348 -0.396259982 0.264557477 -1.074885909 0.174385353
[51] 0.055591941 1.288138677 0.794117417 0.869098487 -0.470878788
[56] -0.270979002 0.249125854 0.236288970 0.494885010 0.746430323
[61] -1.375718452 0.702513001 0.961848988 0.008218281 0.846459448
[66] 0.570249601 1.206156350 0.539742743 -0.035273770 -0.221343121
[71] 2.064022223 -0.223729411 0.385658425 0.334225746 -0.573454095
[76] 1.745283146 1.234005193 1.047301603 0.039672661 2.014898039
[81] -1.943840541 -0.662198182 -0.015978531 -0.523450004 -1.285554926
[86] 1.044646520 1.485137045 0.506525990 -1.719657900 1.374694331
[91] 0.575192025 -0.043405404 -2.013608685 0.564385727 0.568201853
[96] 1.204391013 -0.540394201 0.850014494 0.316852466 0.765689295
> colMedians(tmp)
[1] -0.029569253 -0.455893959 -0.912238300 2.030428553 1.224819981
[6] 0.625973391 -0.493234012 0.201082653 1.575461399 -0.375206173
[11] -0.623138120 0.154108909 0.365052760 -1.032278860 -1.347545787
[16] 3.189975846 -1.138193312 0.986702383 -2.196979489 0.355505743
[21] 1.716610508 -0.527850024 -0.147098747 0.512935731 -0.771844977
[26] 0.718883603 0.452948050 1.659936994 0.934143415 0.562965691
[31] 1.061297862 0.583404359 -1.330257806 -0.903246104 0.545889966
[36] 0.671288399 1.595755976 0.376760919 -1.643041130 0.963625247
[41] 1.655336026 -0.960297797 0.668094860 -0.320270708 0.635927325
[46] 0.314866348 -0.396259982 0.264557477 -1.074885909 0.174385353
[51] 0.055591941 1.288138677 0.794117417 0.869098487 -0.470878788
[56] -0.270979002 0.249125854 0.236288970 0.494885010 0.746430323
[61] -1.375718452 0.702513001 0.961848988 0.008218281 0.846459448
[66] 0.570249601 1.206156350 0.539742743 -0.035273770 -0.221343121
[71] 2.064022223 -0.223729411 0.385658425 0.334225746 -0.573454095
[76] 1.745283146 1.234005193 1.047301603 0.039672661 2.014898039
[81] -1.943840541 -0.662198182 -0.015978531 -0.523450004 -1.285554926
[86] 1.044646520 1.485137045 0.506525990 -1.719657900 1.374694331
[91] 0.575192025 -0.043405404 -2.013608685 0.564385727 0.568201853
[96] 1.204391013 -0.540394201 0.850014494 0.316852466 0.765689295
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.02956925 -0.455894 -0.9122383 2.030429 1.22482 0.6259734 -0.493234
[2,] -0.02956925 -0.455894 -0.9122383 2.030429 1.22482 0.6259734 -0.493234
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.2010827 1.575461 -0.3752062 -0.6231381 0.1541089 0.3650528 -1.032279
[2,] 0.2010827 1.575461 -0.3752062 -0.6231381 0.1541089 0.3650528 -1.032279
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -1.347546 3.189976 -1.138193 0.9867024 -2.196979 0.3555057 1.716611
[2,] -1.347546 3.189976 -1.138193 0.9867024 -2.196979 0.3555057 1.716611
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -0.52785 -0.1470987 0.5129357 -0.771845 0.7188836 0.452948 1.659937
[2,] -0.52785 -0.1470987 0.5129357 -0.771845 0.7188836 0.452948 1.659937
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.9341434 0.5629657 1.061298 0.5834044 -1.330258 -0.9032461 0.54589
[2,] 0.9341434 0.5629657 1.061298 0.5834044 -1.330258 -0.9032461 0.54589
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.6712884 1.595756 0.3767609 -1.643041 0.9636252 1.655336 -0.9602978
[2,] 0.6712884 1.595756 0.3767609 -1.643041 0.9636252 1.655336 -0.9602978
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 0.6680949 -0.3202707 0.6359273 0.3148663 -0.39626 0.2645575 -1.074886
[2,] 0.6680949 -0.3202707 0.6359273 0.3148663 -0.39626 0.2645575 -1.074886
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.1743854 0.05559194 1.288139 0.7941174 0.8690985 -0.4708788 -0.270979
[2,] 0.1743854 0.05559194 1.288139 0.7941174 0.8690985 -0.4708788 -0.270979
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 0.2491259 0.236289 0.494885 0.7464303 -1.375718 0.702513 0.961849
[2,] 0.2491259 0.236289 0.494885 0.7464303 -1.375718 0.702513 0.961849
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.008218281 0.8464594 0.5702496 1.206156 0.5397427 -0.03527377 -0.2213431
[2,] 0.008218281 0.8464594 0.5702496 1.206156 0.5397427 -0.03527377 -0.2213431
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] 2.064022 -0.2237294 0.3856584 0.3342257 -0.5734541 1.745283 1.234005
[2,] 2.064022 -0.2237294 0.3856584 0.3342257 -0.5734541 1.745283 1.234005
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 1.047302 0.03967266 2.014898 -1.943841 -0.6621982 -0.01597853 -0.52345
[2,] 1.047302 0.03967266 2.014898 -1.943841 -0.6621982 -0.01597853 -0.52345
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] -1.285555 1.044647 1.485137 0.506526 -1.719658 1.374694 0.575192
[2,] -1.285555 1.044647 1.485137 0.506526 -1.719658 1.374694 0.575192
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -0.0434054 -2.013609 0.5643857 0.5682019 1.204391 -0.5403942 0.8500145
[2,] -0.0434054 -2.013609 0.5643857 0.5682019 1.204391 -0.5403942 0.8500145
[,99] [,100]
[1,] 0.3168525 0.7656893
[2,] 0.3168525 0.7656893
>
>
> Max(tmp2)
[1] 3.410111
> Min(tmp2)
[1] -2.000276
> mean(tmp2)
[1] -0.01341615
> Sum(tmp2)
[1] -1.341615
> Var(tmp2)
[1] 1.212185
>
> rowMeans(tmp2)
[1] 0.70184703 -0.73693318 0.41777846 0.94997425 0.29571466 1.26842335
[7] 1.94467196 -0.32500656 -1.46378360 0.01965425 0.78831077 1.63757381
[13] -1.15133591 -1.03511329 -0.24619010 2.23662451 3.41011130 0.86193011
[19] 2.08733866 -0.11941915 -1.40555736 2.08505161 -0.48970511 1.04642628
[25] -0.92809606 -1.99925476 0.36670488 0.27892429 0.26184424 -0.57515990
[31] -0.93934664 -0.87711259 0.67398074 0.94193013 -0.41354148 -1.85399010
[37] -0.92753080 0.32558408 0.15765991 -1.34777330 2.01824232 -1.72547305
[43] -0.96699780 -0.52712640 -0.25190196 -0.43969489 0.68049823 0.83282433
[49] 0.29505389 1.01506477 0.27944229 0.58825252 -0.03071199 -0.57851061
[55] 1.56402181 0.24086236 -0.05612880 2.58775104 -0.02271461 -1.34606256
[61] -0.56127926 -1.27620018 -0.94698540 1.42737158 0.22406337 0.66264812
[67] -1.49414080 1.38433100 -0.31060119 -0.14415892 0.81736820 -1.81599644
[73] -0.34020210 -0.79603337 0.03718241 -0.03176025 0.49202742 -1.60210461
[79] 0.99651929 -2.00027593 -0.30546421 -0.38272476 0.08641284 -1.27799314
[85] 0.88013769 -1.20904203 0.85121820 -1.65673531 -0.67852985 -0.68159917
[91] -0.79948735 -1.11333058 -0.97988815 -0.97170536 0.76437096 0.89097596
[97] 0.07535716 0.95434655 0.27730795 -0.86691555
> rowSums(tmp2)
[1] 0.70184703 -0.73693318 0.41777846 0.94997425 0.29571466 1.26842335
[7] 1.94467196 -0.32500656 -1.46378360 0.01965425 0.78831077 1.63757381
[13] -1.15133591 -1.03511329 -0.24619010 2.23662451 3.41011130 0.86193011
[19] 2.08733866 -0.11941915 -1.40555736 2.08505161 -0.48970511 1.04642628
[25] -0.92809606 -1.99925476 0.36670488 0.27892429 0.26184424 -0.57515990
[31] -0.93934664 -0.87711259 0.67398074 0.94193013 -0.41354148 -1.85399010
[37] -0.92753080 0.32558408 0.15765991 -1.34777330 2.01824232 -1.72547305
[43] -0.96699780 -0.52712640 -0.25190196 -0.43969489 0.68049823 0.83282433
[49] 0.29505389 1.01506477 0.27944229 0.58825252 -0.03071199 -0.57851061
[55] 1.56402181 0.24086236 -0.05612880 2.58775104 -0.02271461 -1.34606256
[61] -0.56127926 -1.27620018 -0.94698540 1.42737158 0.22406337 0.66264812
[67] -1.49414080 1.38433100 -0.31060119 -0.14415892 0.81736820 -1.81599644
[73] -0.34020210 -0.79603337 0.03718241 -0.03176025 0.49202742 -1.60210461
[79] 0.99651929 -2.00027593 -0.30546421 -0.38272476 0.08641284 -1.27799314
[85] 0.88013769 -1.20904203 0.85121820 -1.65673531 -0.67852985 -0.68159917
[91] -0.79948735 -1.11333058 -0.97988815 -0.97170536 0.76437096 0.89097596
[97] 0.07535716 0.95434655 0.27730795 -0.86691555
> 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] 0.70184703 -0.73693318 0.41777846 0.94997425 0.29571466 1.26842335
[7] 1.94467196 -0.32500656 -1.46378360 0.01965425 0.78831077 1.63757381
[13] -1.15133591 -1.03511329 -0.24619010 2.23662451 3.41011130 0.86193011
[19] 2.08733866 -0.11941915 -1.40555736 2.08505161 -0.48970511 1.04642628
[25] -0.92809606 -1.99925476 0.36670488 0.27892429 0.26184424 -0.57515990
[31] -0.93934664 -0.87711259 0.67398074 0.94193013 -0.41354148 -1.85399010
[37] -0.92753080 0.32558408 0.15765991 -1.34777330 2.01824232 -1.72547305
[43] -0.96699780 -0.52712640 -0.25190196 -0.43969489 0.68049823 0.83282433
[49] 0.29505389 1.01506477 0.27944229 0.58825252 -0.03071199 -0.57851061
[55] 1.56402181 0.24086236 -0.05612880 2.58775104 -0.02271461 -1.34606256
[61] -0.56127926 -1.27620018 -0.94698540 1.42737158 0.22406337 0.66264812
[67] -1.49414080 1.38433100 -0.31060119 -0.14415892 0.81736820 -1.81599644
[73] -0.34020210 -0.79603337 0.03718241 -0.03176025 0.49202742 -1.60210461
[79] 0.99651929 -2.00027593 -0.30546421 -0.38272476 0.08641284 -1.27799314
[85] 0.88013769 -1.20904203 0.85121820 -1.65673531 -0.67852985 -0.68159917
[91] -0.79948735 -1.11333058 -0.97988815 -0.97170536 0.76437096 0.89097596
[97] 0.07535716 0.95434655 0.27730795 -0.86691555
> rowMin(tmp2)
[1] 0.70184703 -0.73693318 0.41777846 0.94997425 0.29571466 1.26842335
[7] 1.94467196 -0.32500656 -1.46378360 0.01965425 0.78831077 1.63757381
[13] -1.15133591 -1.03511329 -0.24619010 2.23662451 3.41011130 0.86193011
[19] 2.08733866 -0.11941915 -1.40555736 2.08505161 -0.48970511 1.04642628
[25] -0.92809606 -1.99925476 0.36670488 0.27892429 0.26184424 -0.57515990
[31] -0.93934664 -0.87711259 0.67398074 0.94193013 -0.41354148 -1.85399010
[37] -0.92753080 0.32558408 0.15765991 -1.34777330 2.01824232 -1.72547305
[43] -0.96699780 -0.52712640 -0.25190196 -0.43969489 0.68049823 0.83282433
[49] 0.29505389 1.01506477 0.27944229 0.58825252 -0.03071199 -0.57851061
[55] 1.56402181 0.24086236 -0.05612880 2.58775104 -0.02271461 -1.34606256
[61] -0.56127926 -1.27620018 -0.94698540 1.42737158 0.22406337 0.66264812
[67] -1.49414080 1.38433100 -0.31060119 -0.14415892 0.81736820 -1.81599644
[73] -0.34020210 -0.79603337 0.03718241 -0.03176025 0.49202742 -1.60210461
[79] 0.99651929 -2.00027593 -0.30546421 -0.38272476 0.08641284 -1.27799314
[85] 0.88013769 -1.20904203 0.85121820 -1.65673531 -0.67852985 -0.68159917
[91] -0.79948735 -1.11333058 -0.97988815 -0.97170536 0.76437096 0.89097596
[97] 0.07535716 0.95434655 0.27730795 -0.86691555
>
> colMeans(tmp2)
[1] -0.01341615
> colSums(tmp2)
[1] -1.341615
> colVars(tmp2)
[1] 1.212185
> colSd(tmp2)
[1] 1.100993
> colMax(tmp2)
[1] 3.410111
> colMin(tmp2)
[1] -2.000276
> colMedians(tmp2)
[1] -0.03123612
> colRanges(tmp2)
[,1]
[1,] -2.000276
[2,] 3.410111
>
> 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] 0.71055964 2.28045565 0.03521655 3.86762902 0.73903713 -2.48691540
[7] -0.90263251 1.39421151 3.29651679 -3.13839510
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.6780228
[2,] -0.5169769
[3,] 0.4644579
[4,] 0.6680420
[5,] 0.7252694
>
> rowApply(tmp,sum)
[1] -0.006090805 2.174063522 -0.198807634 4.517091487 -7.255277806
[6] 3.862048195 3.208944630 -5.106525834 0.160962120 4.439275420
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 8 8 7 3 5 6 9 7 1
[2,] 10 2 5 9 2 6 3 4 8 9
[3,] 6 10 1 10 4 2 5 5 3 5
[4,] 8 1 3 4 9 9 7 8 9 8
[5,] 7 6 6 8 5 4 4 6 6 3
[6,] 9 3 4 3 10 10 2 2 2 4
[7,] 5 5 7 6 7 1 9 1 4 2
[8,] 4 7 10 2 1 8 10 7 1 7
[9,] 2 9 2 5 6 3 8 10 10 10
[10,] 3 4 9 1 8 7 1 3 5 6
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -2.3621895 1.4557453 -0.2077139 2.6505826 -1.5242001 -1.2028307
[7] -1.1076806 -2.7551582 4.7047741 1.0920064 1.4893398 -0.2377362
[13] -4.8678240 -2.3953733 -2.3139056 3.1638102 -0.5997575 -3.4509311
[19] 2.6246896 3.3498041
> colApply(tmp,quantile)[,1]
[,1]
[1,] -2.7167417
[2,] -0.6256092
[3,] -0.5076424
[4,] 0.2180236
[5,] 1.2697802
>
> rowApply(tmp,sum)
[1] -4.22652986 -5.75499866 0.03365988 4.09294485 3.36037502
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 6 7 19 1 11
[2,] 13 8 17 12 15
[3,] 19 3 10 13 3
[4,] 17 13 16 17 18
[5,] 10 12 15 8 1
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.6256092 0.03957423 1.58895310 0.4504289 -0.26284558 -0.6449499
[2,] -0.5076424 -0.47855915 -1.50165624 -0.0268760 -0.16502120 0.4695756
[3,] 1.2697802 0.68808748 0.01329984 0.3692051 0.23666166 -0.7026272
[4,] -2.7167417 0.52698538 0.53732235 0.8958484 0.05145828 0.3706442
[5,] 0.2180236 0.67965733 -0.84563297 0.9619762 -1.38445328 -0.6954734
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.3470676 -0.8269463 -0.5734891 1.7043569 0.1458745 -0.03533090
[2,] -1.8801231 -0.3896092 0.1969968 -1.1815798 -0.3630763 0.02798236
[3,] 0.1279190 -0.6444345 1.4396268 -0.0918375 -0.7775723 -0.16522822
[4,] -0.4195015 -0.6959735 2.6879491 0.9091330 -0.5935508 -0.56374285
[5,] 1.4110925 -0.1981948 0.9536905 -0.2480661 3.0776648 0.49858340
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -2.7205231 -2.0147204 -0.2921463 0.90635649 0.3967763 -1.18913727
[2,] -1.6092811 -0.3965588 -0.8436372 1.63048508 0.1391618 -1.21001374
[3,] -1.4955370 -0.1598392 -1.0274439 0.15411812 0.1152037 0.07013001
[4,] 0.1734867 0.7027098 0.2850670 0.55184064 -0.1492205 -0.32105867
[5,] 0.7840304 -0.5269648 -0.4357453 -0.07899009 -1.1016789 -0.80085142
[,19] [,20]
[1,] -0.1560375 0.2299529
[2,] 0.3679537 1.9664802
[3,] 0.9334640 -0.3193163
[4,] 0.8139357 1.0463536
[5,] 0.6653738 0.4263336
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-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-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 653 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-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: /home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 480 bytes.
>
>
> rm(tmp)
>
>
> ###
> ### Testing colnames and rownames
> ###
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
>
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7
row1 -0.206714 -0.3154795 2.443762 1.247449 2.12329 -0.09096546 -1.172678
col8 col9 col10 col11 col12 col13 col14
row1 -0.5165748 3.213379 -0.8108569 -0.7549488 -0.3956142 -1.015855 -1.589886
col15 col16 col17 col18 col19 col20
row1 -1.482087 1.280585 -0.2977507 -0.3720588 -0.05649995 -1.386998
> tmp[,"col10"]
col10
row1 -0.8108569
row2 0.6549282
row3 -2.3706401
row4 -0.2126308
row5 -0.9927899
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 -0.2067140 -0.3154795 2.4437624 1.247449 2.123290 -0.09096546 -1.172678
row5 -0.9693648 1.6031306 0.3426948 1.649600 -1.261596 0.97378407 -1.905228
col8 col9 col10 col11 col12 col13
row1 -0.5165748 3.2133786 -0.8108569 -0.7549488 -0.3956142 -1.01585491
row5 -0.1007948 -0.7383055 -0.9927899 -0.7497374 -0.2691522 0.09408999
col14 col15 col16 col17 col18 col19 col20
row1 -1.589886 -1.482087 1.280585 -0.2977507 -0.3720588 -0.05649995 -1.3869981
row5 -1.269281 -1.105310 -2.019006 -0.4314419 -0.6207416 -0.90415965 0.5147915
> tmp[,c("col6","col20")]
col6 col20
row1 -0.09096546 -1.38699809
row2 -0.52881165 0.11340232
row3 0.72608738 0.04832108
row4 0.71671518 -0.98155748
row5 0.97378407 0.51479152
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -0.09096546 -1.3869981
row5 0.97378407 0.5147915
>
>
>
>
> tmp["row1",] <- rnorm(20,mean=10)
> tmp[,"col10"] <- rnorm(5,mean=30)
> tmp[c("row1","row5"),] <- rnorm(40,mean=50)
> tmp[,c("col6","col20")] <- rnorm(10,mean=75)
> tmp[c("row1","row5"),c("col6","col20")] <- rnorm(4,mean=105)
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.40811 50.20756 50.21541 51.28991 51.0662 105.3223 51.42976 48.40832
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.49957 48.98434 50.10154 48.5066 50.89875 50.27546 52.05377 50.07721
col17 col18 col19 col20
row1 49.17705 48.77168 50.04304 105.644
> tmp[,"col10"]
col10
row1 48.98434
row2 29.16126
row3 28.68147
row4 30.53546
row5 48.55225
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.40811 50.20756 50.21541 51.28991 51.06620 105.3223 51.42976 48.40832
row5 50.86132 48.86777 51.36799 50.30220 50.13002 105.6246 48.47251 50.91866
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.49957 48.98434 50.10154 48.50660 50.89875 50.27546 52.05377 50.07721
row5 49.95475 48.55225 49.51146 51.43066 49.62887 51.25247 51.75084 48.95228
col17 col18 col19 col20
row1 49.17705 48.77168 50.04304 105.6440
row5 50.09392 50.31694 52.41983 104.7315
> tmp[,c("col6","col20")]
col6 col20
row1 105.32231 105.64400
row2 74.29006 74.93292
row3 74.37353 76.41941
row4 74.88273 75.28012
row5 105.62455 104.73154
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 105.3223 105.6440
row5 105.6246 104.7315
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 105.3223 105.6440
row5 105.6246 104.7315
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -1.6044842
[2,] 1.5400040
[3,] 0.1005510
[4,] -0.8832935
[5,] 0.7904798
> tmp[,c("col17","col7")]
col17 col7
[1,] -1.3854400 -0.3339761
[2,] -1.8479490 -1.7877874
[3,] 1.7622810 -1.0912771
[4,] -0.2852653 0.5965981
[5,] -0.1011070 -1.2574223
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 0.57516525 0.6310187
[2,] -0.44411563 -0.3943040
[3,] -0.59793217 1.4974853
[4,] -1.14630989 -2.3170553
[5,] 0.07293914 0.2977567
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 0.5751653
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 0.5751653
[2,] -0.4441156
>
>
>
> 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 0.4407186 1.1765775 0.8463819 1.108301 0.8426087 0.1895338 0.9059064
row1 0.3395091 -0.9265519 -2.1902201 2.773096 2.1615854 -0.7522474 -0.4650126
[,8] [,9] [,10] [,11] [,12] [,13]
row3 -1.558430 -1.8188164 -1.900682 -0.4233594 0.05700549 -1.35991802
row1 0.239231 -0.3769705 2.026245 0.7265858 -1.86184360 -0.05511561
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row3 1.3178442 -0.7926605 0.8781632 0.6242719 -1.0335112 0.3006278 0.00914531
row1 0.2786169 0.6664010 1.1255890 -0.8849211 0.4218345 1.1044149 -0.86141310
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -0.5895116 -0.3783585 -1.160863 -1.727408 1.099079 1.836511 0.4038392
[,8] [,9] [,10]
row2 -1.151158 1.01808 -1.416558
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.2619603 0.1690183 0.9731282 -1.18952 -0.2552008 -0.3648472 -1.630606
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 0.4389644 -1.060287 0.3856071 -0.9597516 0.5972192 -0.4905124 -0.05905566
[,15] [,16] [,17] [,18] [,19] [,20]
row5 1.385877 -0.07363006 0.1899459 -0.3865157 -0.5280757 1.068827
>
>
> 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: 0x5816ab7dd650>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM23ae5464a2b074"
[2] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM23ae547766dfee"
[3] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM23ae5472e49ce2"
[4] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM23ae543998459d"
[5] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM23ae5459e9720f"
[6] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM23ae54508dad25"
[7] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM23ae5474514fca"
[8] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM23ae54440734a4"
[9] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM23ae5486d868"
[10] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM23ae54713e800e"
[11] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM23ae5423a1e49a"
[12] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM23ae5477a2314b"
[13] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM23ae54698f3ad5"
[14] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM23ae543e74d1fd"
[15] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM23ae543c08e78b"
>
>
> ### 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: 0x5816abcc49b0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x5816abcc49b0>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x5816abcc49b0>
> rowMedians(tmp)
[1] 0.148947783 -0.094728893 0.176698746 0.378901330 -0.402722536
[6] -0.241233666 -0.166479270 0.195455912 -0.161534893 0.366627733
[11] -0.110757845 0.220109087 -0.052054708 -0.158564111 -0.373754627
[16] 0.719289865 0.042849815 0.258607779 -0.140989829 0.145830873
[21] 0.342759477 -0.394112087 -0.189588334 0.442152548 -0.501678156
[26] -0.434607031 -0.336783514 -0.618397083 0.014944571 -0.030319226
[31] 0.107455857 -0.146850567 0.035751048 -0.214977355 0.237474140
[36] 0.814180278 -0.507951604 0.080503002 -0.269471938 -0.023984020
[41] 0.111785863 -0.151496976 -0.466270301 0.361047751 -0.057122758
[46] 0.007843848 -0.507603626 0.264346035 -0.147651869 -0.034270082
[51] 0.428960521 0.154209002 0.182143934 0.006724675 -0.202305617
[56] -0.199036722 -0.065080393 -0.284336702 -0.501386615 -0.178557337
[61] -0.288727800 0.153999288 -0.427555249 -0.029074491 -0.672343131
[66] -0.057946630 -0.220281959 0.274800277 0.338352726 0.510901995
[71] -0.394398098 0.063216387 -0.314597133 0.260035438 -0.625067361
[76] 0.358548889 0.104088956 -0.689150704 -0.369790230 -0.619780928
[81] 0.051591297 -0.776019575 -0.080020246 0.468158132 -0.136152364
[86] 0.476457667 0.678828170 -0.286054257 0.251028045 -0.423736283
[91] -0.212059951 -0.152408278 -0.513788674 0.085958669 -0.140651351
[96] -0.009570516 -0.072331247 -0.410571145 0.064744442 0.325178501
[101] 0.241585141 0.310498079 -0.301412394 0.095428513 -0.216288045
[106] 0.005391549 -0.130425599 0.143532064 -0.059822872 -0.073666558
[111] 0.514835967 -0.221161465 -0.043716095 0.498389491 -0.437655568
[116] 0.388492272 0.184088512 0.274895083 -0.544321567 0.283208828
[121] 0.449635608 0.062840300 -0.412219170 -0.156648380 0.223979953
[126] 0.387402002 -0.070068612 0.001462694 0.595069976 0.003277919
[131] 0.457757226 0.388839075 -0.382056850 -0.055829948 0.027836637
[136] 0.011478539 0.082441565 0.175150885 -0.033462912 -0.127232314
[141] 0.267518472 0.466331716 0.190987204 0.532876182 0.199615221
[146] 0.560676471 -0.232191483 -0.324352891 -0.173733579 -0.019990195
[151] -0.795407922 -0.083215418 -0.117161625 0.294367861 0.060477757
[156] 0.558562210 0.100130248 0.256256031 0.130983084 0.404716636
[161] 0.131184798 0.102435110 0.269966227 -0.145091690 0.285947180
[166] -0.445609800 0.006800940 0.019803402 0.040522437 -0.108047957
[171] -0.318183409 -0.615582986 -0.219947293 -0.752607143 0.188342628
[176] 0.006095643 -0.217507199 -0.274350294 -0.126085376 -0.291710676
[181] 0.142220168 0.493943353 0.373669225 -0.402843764 0.226116619
[186] -0.329992797 0.297964761 0.221015349 0.315228131 0.052692824
[191] -0.176378374 -0.222831614 -0.327155033 0.416390374 0.604575566
[196] 0.329372988 -0.052856078 -0.100207995 0.388325648 0.298337560
[201] -0.492065796 -0.034663758 -0.426151147 0.136707426 0.279436040
[206] 0.262017288 0.004219002 0.801155199 -0.141615427 0.339372580
[211] -0.034935507 0.214017158 0.053919216 -0.020882808 0.333898024
[216] 0.755183673 -0.265741426 -0.554862505 0.151529261 0.041488480
[221] -0.311361043 0.309030181 0.524901855 -0.521603930 0.498036453
[226] -0.079345703 0.048714454 0.062933192 0.144467569 0.173328816
>
> proc.time()
user system elapsed
1.316 1.553 2.859
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-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: 0x571a452d00f0>
> .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: 0x571a452d00f0>
> .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: 0x571a452d00f0>
> .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: 0x571a452d00f0>
> 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: 0x571a4611e690>
> .Call("R_bm_AddColumn",P)
<pointer: 0x571a4611e690>
> .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: 0x571a4611e690>
> .Call("R_bm_AddColumn",P)
<pointer: 0x571a4611e690>
> .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: 0x571a4611e690>
> 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: 0x571a47b58010>
> .Call("R_bm_AddColumn",P)
<pointer: 0x571a47b58010>
> .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: 0x571a47b58010>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x571a47b58010>
> .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: 0x571a47b58010>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x571a47b58010>
> .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: 0x571a47b58010>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x571a47b58010>
> .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: 0x571a47b58010>
> 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: 0x571a47ba8070>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x571a47ba8070>
> .Call("R_bm_AddColumn",P)
<pointer: 0x571a47ba8070>
> .Call("R_bm_AddColumn",P)
<pointer: 0x571a47ba8070>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile23b06741cd23ba" "BufferedMatrixFile23b0676f2c3f49"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile23b06741cd23ba" "BufferedMatrixFile23b0676f2c3f49"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x571a458627e0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x571a458627e0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x571a458627e0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x571a458627e0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x571a458627e0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x571a458627e0>
> .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: 0x571a477fe3b0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x571a477fe3b0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x571a477fe3b0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x571a477fe3b0>
> 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: 0x571a459c4520>
> .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: 0x571a459c4520>
> rm(P)
>
> proc.time()
user system elapsed
0.239 0.057 0.285
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
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> 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
0.236 0.049 0.273