Ben Bolstad
| Snapshot Date: 2026-03-06 13:45 -0500 (Fri, 06 Mar 2026) |
| 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 Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-07 11:57 -0500 (Sat, 07 Mar 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" | 4892 |
| 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 | | ||||||||
| 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: 1.74.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BufferedMatrix_1.74.0.tar.gz |
| StartedAt: 2026-03-06 21:55:32 -0500 (Fri, 06 Mar 2026) |
| EndedAt: 2026-03-06 21:55:55 -0500 (Fri, 06 Mar 2026) |
| EllapsedTime: 23.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BufferedMatrix_1.74.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 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 ... 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 re-building of vignette outputs ... OK
* 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
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.74.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-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-3.22-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-3.22-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-3.22-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-3.22-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-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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
0.289 0.044 0.322
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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-3.22-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 478284 25.6 1046725 56 639600 34.2
Vcells 884773 6.8 8388608 64 2081613 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] "Fri Mar 6 21:55:46 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] "Fri Mar 6 21:55:46 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: 0x64025fd6c370>
>
>
>
> 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] "Fri Mar 6 21:55:47 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] "Fri Mar 6 21:55:47 2026"
>
> ColMode(tmp2)
<pointer: 0x64025fd6c370>
>
>
>
> ### 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,] 101.1005502 0.81689606 -0.31615977 0.9477056
[2,] -0.3910712 1.40308318 -0.75203686 -0.9805217
[3,] 0.4327614 -0.01799499 -0.06246976 -0.6030938
[4,] -0.0433761 1.44459048 -1.36442224 -0.9118296
> 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 : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 101.1005502 0.81689606 0.31615977 0.9477056
[2,] 0.3910712 1.40308318 0.75203686 0.9805217
[3,] 0.4327614 0.01799499 0.06246976 0.6030938
[4,] 0.0433761 1.44459048 1.36442224 0.9118296
> 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 : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 10.0548769 0.9038230 0.5622809 0.9735017
[2,] 0.6253569 1.1845181 0.8672006 0.9902129
[3,] 0.6578460 0.1341454 0.2499395 0.7765911
[4,] 0.2082693 1.2019112 1.1680849 0.9548977
>
> 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 : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 226.64932 34.85513 30.93897 35.68272
[2,] 31.64464 38.24826 34.42404 35.88265
[3,] 32.01122 26.35945 27.56186 33.36900
[4,] 27.12607 38.46370 38.04527 35.46081
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x640260d689b0>
> exp(tmp5)
<pointer: 0x640260d689b0>
> log(tmp5,2)
<pointer: 0x640260d689b0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 471.7409
> Min(tmp5)
[1] 54.54831
> mean(tmp5)
[1] 72.54959
> Sum(tmp5)
[1] 14509.92
> Var(tmp5)
[1] 883.6873
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 92.13814 69.74225 68.25353 73.15555 69.43249 74.20836 67.22987 71.31537
[9] 69.03496 70.98536
> rowSums(tmp5)
[1] 1842.763 1394.845 1365.071 1463.111 1388.650 1484.167 1344.597 1426.307
[9] 1380.699 1419.707
> rowVars(tmp5)
[1] 8031.11087 106.65024 68.19730 81.19765 80.87063 97.31811
[7] 42.26722 59.03621 101.42110 95.28134
> rowSd(tmp5)
[1] 89.616465 10.327160 8.258166 9.010974 8.992810 9.864994 6.501324
[8] 7.683503 10.070805 9.761216
> rowMax(tmp5)
[1] 471.74086 91.84656 86.06215 86.62495 84.60339 95.39702 81.97893
[8] 87.88222 96.58558 95.90029
> rowMin(tmp5)
[1] 55.00744 56.76804 54.86374 56.45936 54.54831 58.13032 56.93759 59.61017
[9] 55.05809 56.67624
>
> colMeans(tmp5)
[1] 107.40798 73.40866 66.21046 72.23869 70.40319 69.10179 75.00079
[8] 69.15162 70.19777 69.35102 71.21000 69.96509 69.84593 69.58064
[15] 67.61033 71.05893 74.99414 75.76046 67.42292 71.07135
> colSums(tmp5)
[1] 1074.0798 734.0866 662.1046 722.3869 704.0319 691.0179 750.0079
[8] 691.5162 701.9777 693.5102 712.1000 699.6509 698.4593 695.8064
[15] 676.1033 710.5893 749.9414 757.6046 674.2292 710.7135
> colVars(tmp5)
[1] 16447.51436 92.72091 51.40330 38.01716 85.50297 87.29132
[7] 21.62426 89.63291 84.17874 58.68970 66.66799 117.13459
[13] 102.73396 68.23101 89.83767 150.73808 127.01484 93.64156
[19] 47.27792 61.78025
> colSd(tmp5)
[1] 128.247863 9.629169 7.169609 6.165806 9.246781 9.342982
[7] 4.650189 9.467466 9.174898 7.660920 8.165047 10.822873
[13] 10.135776 8.260207 9.478274 12.277544 11.270086 9.676857
[19] 6.875894 7.860041
> colMax(tmp5)
[1] 471.74086 84.46119 79.18625 84.60339 82.72018 91.84656 80.95485
[8] 81.97893 84.63612 82.19071 85.45727 95.90029 86.46975 79.78396
[15] 86.06215 94.52272 96.58558 95.39702 76.83493 83.17498
> colMin(tmp5)
[1] 56.45936 54.86374 56.67624 65.10837 57.02440 61.14367 64.53479 56.79470
[9] 56.93759 56.76804 59.91781 58.29397 58.13032 55.05809 54.54831 55.00744
[17] 61.58584 63.51348 55.22908 59.40598
>
>
> ### 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] 92.13814 69.74225 NA 73.15555 69.43249 74.20836 67.22987 71.31537
[9] 69.03496 70.98536
> rowSums(tmp5)
[1] 1842.763 1394.845 NA 1463.111 1388.650 1484.167 1344.597 1426.307
[9] 1380.699 1419.707
> rowVars(tmp5)
[1] 8031.11087 106.65024 71.14828 81.19765 80.87063 97.31811
[7] 42.26722 59.03621 101.42110 95.28134
> rowSd(tmp5)
[1] 89.616465 10.327160 8.434944 9.010974 8.992810 9.864994 6.501324
[8] 7.683503 10.070805 9.761216
> rowMax(tmp5)
[1] 471.74086 91.84656 NA 86.62495 84.60339 95.39702 81.97893
[8] 87.88222 96.58558 95.90029
> rowMin(tmp5)
[1] 55.00744 56.76804 NA 56.45936 54.54831 58.13032 56.93759 59.61017
[9] 55.05809 56.67624
>
> colMeans(tmp5)
[1] 107.40798 73.40866 66.21046 72.23869 70.40319 NA 75.00079
[8] 69.15162 70.19777 69.35102 71.21000 69.96509 69.84593 69.58064
[15] 67.61033 71.05893 74.99414 75.76046 67.42292 71.07135
> colSums(tmp5)
[1] 1074.0798 734.0866 662.1046 722.3869 704.0319 NA 750.0079
[8] 691.5162 701.9777 693.5102 712.1000 699.6509 698.4593 695.8064
[15] 676.1033 710.5893 749.9414 757.6046 674.2292 710.7135
> colVars(tmp5)
[1] 16447.51436 92.72091 51.40330 38.01716 85.50297 NA
[7] 21.62426 89.63291 84.17874 58.68970 66.66799 117.13459
[13] 102.73396 68.23101 89.83767 150.73808 127.01484 93.64156
[19] 47.27792 61.78025
> colSd(tmp5)
[1] 128.247863 9.629169 7.169609 6.165806 9.246781 NA
[7] 4.650189 9.467466 9.174898 7.660920 8.165047 10.822873
[13] 10.135776 8.260207 9.478274 12.277544 11.270086 9.676857
[19] 6.875894 7.860041
> colMax(tmp5)
[1] 471.74086 84.46119 79.18625 84.60339 82.72018 NA 80.95485
[8] 81.97893 84.63612 82.19071 85.45727 95.90029 86.46975 79.78396
[15] 86.06215 94.52272 96.58558 95.39702 76.83493 83.17498
> colMin(tmp5)
[1] 56.45936 54.86374 56.67624 65.10837 57.02440 NA 64.53479 56.79470
[9] 56.93759 56.76804 59.91781 58.29397 58.13032 55.05809 54.54831 55.00744
[17] 61.58584 63.51348 55.22908 59.40598
>
> Max(tmp5,na.rm=TRUE)
[1] 471.7409
> Min(tmp5,na.rm=TRUE)
[1] 54.54831
> mean(tmp5,na.rm=TRUE)
[1] 72.5902
> Sum(tmp5,na.rm=TRUE)
[1] 14445.45
> Var(tmp5,na.rm=TRUE)
[1] 887.8189
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.13814 69.74225 68.45273 73.15555 69.43249 74.20836 67.22987 71.31537
[9] 69.03496 70.98536
> rowSums(tmp5,na.rm=TRUE)
[1] 1842.763 1394.845 1300.602 1463.111 1388.650 1484.167 1344.597 1426.307
[9] 1380.699 1419.707
> rowVars(tmp5,na.rm=TRUE)
[1] 8031.11087 106.65024 71.14828 81.19765 80.87063 97.31811
[7] 42.26722 59.03621 101.42110 95.28134
> rowSd(tmp5,na.rm=TRUE)
[1] 89.616465 10.327160 8.434944 9.010974 8.992810 9.864994 6.501324
[8] 7.683503 10.070805 9.761216
> rowMax(tmp5,na.rm=TRUE)
[1] 471.74086 91.84656 86.06215 86.62495 84.60339 95.39702 81.97893
[8] 87.88222 96.58558 95.90029
> rowMin(tmp5,na.rm=TRUE)
[1] 55.00744 56.76804 54.86374 56.45936 54.54831 58.13032 56.93759 59.61017
[9] 55.05809 56.67624
>
> colMeans(tmp5,na.rm=TRUE)
[1] 107.40798 73.40866 66.21046 72.23869 70.40319 69.61659 75.00079
[8] 69.15162 70.19777 69.35102 71.21000 69.96509 69.84593 69.58064
[15] 67.61033 71.05893 74.99414 75.76046 67.42292 71.07135
> colSums(tmp5,na.rm=TRUE)
[1] 1074.0798 734.0866 662.1046 722.3869 704.0319 626.5493 750.0079
[8] 691.5162 701.9777 693.5102 712.1000 699.6509 698.4593 695.8064
[15] 676.1033 710.5893 749.9414 757.6046 674.2292 710.7135
> colVars(tmp5,na.rm=TRUE)
[1] 16447.51436 92.72091 51.40330 38.01716 85.50297 95.22127
[7] 21.62426 89.63291 84.17874 58.68970 66.66799 117.13459
[13] 102.73396 68.23101 89.83767 150.73808 127.01484 93.64156
[19] 47.27792 61.78025
> colSd(tmp5,na.rm=TRUE)
[1] 128.247863 9.629169 7.169609 6.165806 9.246781 9.758138
[7] 4.650189 9.467466 9.174898 7.660920 8.165047 10.822873
[13] 10.135776 8.260207 9.478274 12.277544 11.270086 9.676857
[19] 6.875894 7.860041
> colMax(tmp5,na.rm=TRUE)
[1] 471.74086 84.46119 79.18625 84.60339 82.72018 91.84656 80.95485
[8] 81.97893 84.63612 82.19071 85.45727 95.90029 86.46975 79.78396
[15] 86.06215 94.52272 96.58558 95.39702 76.83493 83.17498
> colMin(tmp5,na.rm=TRUE)
[1] 56.45936 54.86374 56.67624 65.10837 57.02440 61.14367 64.53479 56.79470
[9] 56.93759 56.76804 59.91781 58.29397 58.13032 55.05809 54.54831 55.00744
[17] 61.58584 63.51348 55.22908 59.40598
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.13814 69.74225 NaN 73.15555 69.43249 74.20836 67.22987 71.31537
[9] 69.03496 70.98536
> rowSums(tmp5,na.rm=TRUE)
[1] 1842.763 1394.845 0.000 1463.111 1388.650 1484.167 1344.597 1426.307
[9] 1380.699 1419.707
> rowVars(tmp5,na.rm=TRUE)
[1] 8031.11087 106.65024 NA 81.19765 80.87063 97.31811
[7] 42.26722 59.03621 101.42110 95.28134
> rowSd(tmp5,na.rm=TRUE)
[1] 89.616465 10.327160 NA 9.010974 8.992810 9.864994 6.501324
[8] 7.683503 10.070805 9.761216
> rowMax(tmp5,na.rm=TRUE)
[1] 471.74086 91.84656 NA 86.62495 84.60339 95.39702 81.97893
[8] 87.88222 96.58558 95.90029
> rowMin(tmp5,na.rm=TRUE)
[1] 55.00744 56.76804 NA 56.45936 54.54831 58.13032 56.93759 59.61017
[9] 55.05809 56.67624
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 111.93918 75.46920 67.19313 72.54819 71.88972 NaN 76.16368
[8] 69.22990 68.59351 68.92529 70.69239 70.71644 70.26496 69.23916
[15] 65.56013 71.86091 74.85287 77.12123 66.99104 71.67103
> colSums(tmp5,na.rm=TRUE)
[1] 1007.4527 679.2228 604.7382 652.9337 647.0075 0.0000 685.4731
[8] 623.0691 617.3416 620.3277 636.2315 636.4480 632.3847 623.1524
[15] 590.0412 646.7482 673.6758 694.0911 602.9194 645.0392
> colVars(tmp5,na.rm=TRUE)
[1] 18272.470986 56.545197 46.965204 41.691682 71.330851
[6] NA 9.113792 100.768106 65.747468 63.986941
[11] 71.987458 125.425445 113.600293 75.448039 53.779923
[16] 162.344677 142.667165 84.515012 51.089309 65.457199
> colSd(tmp5,na.rm=TRUE)
[1] 135.175704 7.519654 6.853116 6.456910 8.445759 NA
[7] 3.018906 10.038332 8.108481 7.999184 8.484542 11.199350
[13] 10.658344 8.686083 7.333480 12.741455 11.944336 9.193205
[19] 7.147679 8.090562
> colMax(tmp5,na.rm=TRUE)
[1] 471.74086 84.46119 79.18625 84.60339 82.72018 -Inf 80.95485
[8] 81.97893 78.60229 82.19071 85.45727 95.90029 86.46975 79.78396
[15] 76.95059 94.52272 96.58558 95.39702 76.83493 83.17498
> colMin(tmp5,na.rm=TRUE)
[1] 56.45936 60.86009 56.67624 65.10837 59.30688 Inf 70.94380 56.79470
[9] 56.93759 56.76804 59.91781 58.29397 58.13032 55.05809 54.54831 55.00744
[17] 61.58584 67.95183 55.22908 59.40598
>
>
>
>
> 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] 180.7039 235.7028 151.9621 196.2845 224.8231 169.0797 293.5258 302.1475
[9] 256.5967 221.9728
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 180.7039 235.7028 151.9621 196.2845 224.8231 169.0797 293.5258 302.1475
[9] 256.5967 221.9728
>
>
>
> 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] -1.136868e-13 2.842171e-14 -5.115908e-13 1.136868e-13 -5.684342e-14
[6] -1.705303e-13 -4.547474e-13 -5.684342e-14 0.000000e+00 -8.526513e-14
[11] -5.684342e-14 2.842171e-14 4.263256e-14 7.105427e-15 -5.684342e-14
[16] -2.842171e-14 5.684342e-14 2.842171e-14 -2.842171e-14 -9.947598e-14
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
10 9
5 8
1 7
10 9
9 8
3 15
8 13
10 20
10 16
1 15
10 19
9 7
3 18
7 8
2 20
2 6
2 1
9 2
5 10
4 2
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> ### now test 1 by n and n by 1 matrix
>
>
> err.tol <- 1e-12
>
> rm(tmp5)
>
> dataset1 <- rnorm(100)
> dataset2 <- rnorm(100)
>
> tmp <- createBufferedMatrix(1,100)
> tmp[1,] <- dataset1
>
> tmp2 <- createBufferedMatrix(100,1)
> tmp2[,1] <- dataset2
>
>
>
>
>
> Max(tmp)
[1] 2.347689
> Min(tmp)
[1] -2.282142
> mean(tmp)
[1] -0.01644119
> Sum(tmp)
[1] -1.644119
> Var(tmp)
[1] 0.9627047
>
> rowMeans(tmp)
[1] -0.01644119
> rowSums(tmp)
[1] -1.644119
> rowVars(tmp)
[1] 0.9627047
> rowSd(tmp)
[1] 0.9811751
> rowMax(tmp)
[1] 2.347689
> rowMin(tmp)
[1] -2.282142
>
> colMeans(tmp)
[1] 1.029100147 1.206004594 1.126915564 1.113811914 -0.723559714
[6] -1.708866786 -1.314986765 0.143574620 0.982927738 -0.807858304
[11] -0.878159090 0.682904832 -0.554650123 2.257289075 -0.245359837
[16] -0.017595230 0.710087564 0.261570001 -0.216107687 -2.282142263
[21] -0.374928266 -0.374015080 0.913788752 -0.089690595 0.237598990
[26] 1.000138154 -0.671066694 -0.758531719 0.712343665 -1.673212652
[31] 1.335289135 -0.356196354 0.230035346 1.274076553 -0.954363830
[36] -0.940528852 0.389668378 0.096064372 0.217882218 -1.109067490
[41] -1.489860285 -0.292876782 1.777552278 -1.371448858 1.790567421
[46] -0.519900458 0.752889698 -0.766103016 0.838650283 0.424190362
[51] 1.761418143 -0.695608532 2.347689266 1.038757440 -1.912649547
[56] -0.322552583 0.540240225 -0.752279277 -0.129996656 0.593285652
[61] -0.389980510 -0.380980089 1.751192461 2.044884565 0.779734694
[66] -0.337104736 -0.360316853 0.008972667 0.485031987 -1.102277393
[71] -0.416822477 -0.018733984 0.426315326 -1.064797223 0.276475739
[76] -1.046786722 -1.134699787 -1.588253162 -0.766637325 0.400204450
[81] 1.158310733 -0.545892247 0.012478310 -0.604559315 0.957864972
[86] -0.533542139 0.496434021 -0.587651760 -1.736093822 -0.480348536
[91] 0.531367748 -0.545244303 -0.123652444 -0.778895114 -1.171674140
[96] 1.026973319 -0.272370516 -0.892762482 0.590966204 0.806601990
> colSums(tmp)
[1] 1.029100147 1.206004594 1.126915564 1.113811914 -0.723559714
[6] -1.708866786 -1.314986765 0.143574620 0.982927738 -0.807858304
[11] -0.878159090 0.682904832 -0.554650123 2.257289075 -0.245359837
[16] -0.017595230 0.710087564 0.261570001 -0.216107687 -2.282142263
[21] -0.374928266 -0.374015080 0.913788752 -0.089690595 0.237598990
[26] 1.000138154 -0.671066694 -0.758531719 0.712343665 -1.673212652
[31] 1.335289135 -0.356196354 0.230035346 1.274076553 -0.954363830
[36] -0.940528852 0.389668378 0.096064372 0.217882218 -1.109067490
[41] -1.489860285 -0.292876782 1.777552278 -1.371448858 1.790567421
[46] -0.519900458 0.752889698 -0.766103016 0.838650283 0.424190362
[51] 1.761418143 -0.695608532 2.347689266 1.038757440 -1.912649547
[56] -0.322552583 0.540240225 -0.752279277 -0.129996656 0.593285652
[61] -0.389980510 -0.380980089 1.751192461 2.044884565 0.779734694
[66] -0.337104736 -0.360316853 0.008972667 0.485031987 -1.102277393
[71] -0.416822477 -0.018733984 0.426315326 -1.064797223 0.276475739
[76] -1.046786722 -1.134699787 -1.588253162 -0.766637325 0.400204450
[81] 1.158310733 -0.545892247 0.012478310 -0.604559315 0.957864972
[86] -0.533542139 0.496434021 -0.587651760 -1.736093822 -0.480348536
[91] 0.531367748 -0.545244303 -0.123652444 -0.778895114 -1.171674140
[96] 1.026973319 -0.272370516 -0.892762482 0.590966204 0.806601990
> 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] 1.029100147 1.206004594 1.126915564 1.113811914 -0.723559714
[6] -1.708866786 -1.314986765 0.143574620 0.982927738 -0.807858304
[11] -0.878159090 0.682904832 -0.554650123 2.257289075 -0.245359837
[16] -0.017595230 0.710087564 0.261570001 -0.216107687 -2.282142263
[21] -0.374928266 -0.374015080 0.913788752 -0.089690595 0.237598990
[26] 1.000138154 -0.671066694 -0.758531719 0.712343665 -1.673212652
[31] 1.335289135 -0.356196354 0.230035346 1.274076553 -0.954363830
[36] -0.940528852 0.389668378 0.096064372 0.217882218 -1.109067490
[41] -1.489860285 -0.292876782 1.777552278 -1.371448858 1.790567421
[46] -0.519900458 0.752889698 -0.766103016 0.838650283 0.424190362
[51] 1.761418143 -0.695608532 2.347689266 1.038757440 -1.912649547
[56] -0.322552583 0.540240225 -0.752279277 -0.129996656 0.593285652
[61] -0.389980510 -0.380980089 1.751192461 2.044884565 0.779734694
[66] -0.337104736 -0.360316853 0.008972667 0.485031987 -1.102277393
[71] -0.416822477 -0.018733984 0.426315326 -1.064797223 0.276475739
[76] -1.046786722 -1.134699787 -1.588253162 -0.766637325 0.400204450
[81] 1.158310733 -0.545892247 0.012478310 -0.604559315 0.957864972
[86] -0.533542139 0.496434021 -0.587651760 -1.736093822 -0.480348536
[91] 0.531367748 -0.545244303 -0.123652444 -0.778895114 -1.171674140
[96] 1.026973319 -0.272370516 -0.892762482 0.590966204 0.806601990
> colMin(tmp)
[1] 1.029100147 1.206004594 1.126915564 1.113811914 -0.723559714
[6] -1.708866786 -1.314986765 0.143574620 0.982927738 -0.807858304
[11] -0.878159090 0.682904832 -0.554650123 2.257289075 -0.245359837
[16] -0.017595230 0.710087564 0.261570001 -0.216107687 -2.282142263
[21] -0.374928266 -0.374015080 0.913788752 -0.089690595 0.237598990
[26] 1.000138154 -0.671066694 -0.758531719 0.712343665 -1.673212652
[31] 1.335289135 -0.356196354 0.230035346 1.274076553 -0.954363830
[36] -0.940528852 0.389668378 0.096064372 0.217882218 -1.109067490
[41] -1.489860285 -0.292876782 1.777552278 -1.371448858 1.790567421
[46] -0.519900458 0.752889698 -0.766103016 0.838650283 0.424190362
[51] 1.761418143 -0.695608532 2.347689266 1.038757440 -1.912649547
[56] -0.322552583 0.540240225 -0.752279277 -0.129996656 0.593285652
[61] -0.389980510 -0.380980089 1.751192461 2.044884565 0.779734694
[66] -0.337104736 -0.360316853 0.008972667 0.485031987 -1.102277393
[71] -0.416822477 -0.018733984 0.426315326 -1.064797223 0.276475739
[76] -1.046786722 -1.134699787 -1.588253162 -0.766637325 0.400204450
[81] 1.158310733 -0.545892247 0.012478310 -0.604559315 0.957864972
[86] -0.533542139 0.496434021 -0.587651760 -1.736093822 -0.480348536
[91] 0.531367748 -0.545244303 -0.123652444 -0.778895114 -1.171674140
[96] 1.026973319 -0.272370516 -0.892762482 0.590966204 0.806601990
> colMedians(tmp)
[1] 1.029100147 1.206004594 1.126915564 1.113811914 -0.723559714
[6] -1.708866786 -1.314986765 0.143574620 0.982927738 -0.807858304
[11] -0.878159090 0.682904832 -0.554650123 2.257289075 -0.245359837
[16] -0.017595230 0.710087564 0.261570001 -0.216107687 -2.282142263
[21] -0.374928266 -0.374015080 0.913788752 -0.089690595 0.237598990
[26] 1.000138154 -0.671066694 -0.758531719 0.712343665 -1.673212652
[31] 1.335289135 -0.356196354 0.230035346 1.274076553 -0.954363830
[36] -0.940528852 0.389668378 0.096064372 0.217882218 -1.109067490
[41] -1.489860285 -0.292876782 1.777552278 -1.371448858 1.790567421
[46] -0.519900458 0.752889698 -0.766103016 0.838650283 0.424190362
[51] 1.761418143 -0.695608532 2.347689266 1.038757440 -1.912649547
[56] -0.322552583 0.540240225 -0.752279277 -0.129996656 0.593285652
[61] -0.389980510 -0.380980089 1.751192461 2.044884565 0.779734694
[66] -0.337104736 -0.360316853 0.008972667 0.485031987 -1.102277393
[71] -0.416822477 -0.018733984 0.426315326 -1.064797223 0.276475739
[76] -1.046786722 -1.134699787 -1.588253162 -0.766637325 0.400204450
[81] 1.158310733 -0.545892247 0.012478310 -0.604559315 0.957864972
[86] -0.533542139 0.496434021 -0.587651760 -1.736093822 -0.480348536
[91] 0.531367748 -0.545244303 -0.123652444 -0.778895114 -1.171674140
[96] 1.026973319 -0.272370516 -0.892762482 0.590966204 0.806601990
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,] 1.0291 1.206005 1.126916 1.113812 -0.7235597 -1.708867 -1.314987 0.1435746
[2,] 1.0291 1.206005 1.126916 1.113812 -0.7235597 -1.708867 -1.314987 0.1435746
[,9] [,10] [,11] [,12] [,13] [,14] [,15]
[1,] 0.9829277 -0.8078583 -0.8781591 0.6829048 -0.5546501 2.257289 -0.2453598
[2,] 0.9829277 -0.8078583 -0.8781591 0.6829048 -0.5546501 2.257289 -0.2453598
[,16] [,17] [,18] [,19] [,20] [,21] [,22]
[1,] -0.01759523 0.7100876 0.26157 -0.2161077 -2.282142 -0.3749283 -0.3740151
[2,] -0.01759523 0.7100876 0.26157 -0.2161077 -2.282142 -0.3749283 -0.3740151
[,23] [,24] [,25] [,26] [,27] [,28] [,29]
[1,] 0.9137888 -0.08969059 0.237599 1.000138 -0.6710667 -0.7585317 0.7123437
[2,] 0.9137888 -0.08969059 0.237599 1.000138 -0.6710667 -0.7585317 0.7123437
[,30] [,31] [,32] [,33] [,34] [,35] [,36]
[1,] -1.673213 1.335289 -0.3561964 0.2300353 1.274077 -0.9543638 -0.9405289
[2,] -1.673213 1.335289 -0.3561964 0.2300353 1.274077 -0.9543638 -0.9405289
[,37] [,38] [,39] [,40] [,41] [,42] [,43]
[1,] 0.3896684 0.09606437 0.2178822 -1.109067 -1.48986 -0.2928768 1.777552
[2,] 0.3896684 0.09606437 0.2178822 -1.109067 -1.48986 -0.2928768 1.777552
[,44] [,45] [,46] [,47] [,48] [,49] [,50]
[1,] -1.371449 1.790567 -0.5199005 0.7528897 -0.766103 0.8386503 0.4241904
[2,] -1.371449 1.790567 -0.5199005 0.7528897 -0.766103 0.8386503 0.4241904
[,51] [,52] [,53] [,54] [,55] [,56] [,57]
[1,] 1.761418 -0.6956085 2.347689 1.038757 -1.91265 -0.3225526 0.5402402
[2,] 1.761418 -0.6956085 2.347689 1.038757 -1.91265 -0.3225526 0.5402402
[,58] [,59] [,60] [,61] [,62] [,63] [,64]
[1,] -0.7522793 -0.1299967 0.5932857 -0.3899805 -0.3809801 1.751192 2.044885
[2,] -0.7522793 -0.1299967 0.5932857 -0.3899805 -0.3809801 1.751192 2.044885
[,65] [,66] [,67] [,68] [,69] [,70] [,71]
[1,] 0.7797347 -0.3371047 -0.3603169 0.008972667 0.485032 -1.102277 -0.4168225
[2,] 0.7797347 -0.3371047 -0.3603169 0.008972667 0.485032 -1.102277 -0.4168225
[,72] [,73] [,74] [,75] [,76] [,77] [,78]
[1,] -0.01873398 0.4263153 -1.064797 0.2764757 -1.046787 -1.1347 -1.588253
[2,] -0.01873398 0.4263153 -1.064797 0.2764757 -1.046787 -1.1347 -1.588253
[,79] [,80] [,81] [,82] [,83] [,84] [,85]
[1,] -0.7666373 0.4002044 1.158311 -0.5458922 0.01247831 -0.6045593 0.957865
[2,] -0.7666373 0.4002044 1.158311 -0.5458922 0.01247831 -0.6045593 0.957865
[,86] [,87] [,88] [,89] [,90] [,91] [,92]
[1,] -0.5335421 0.496434 -0.5876518 -1.736094 -0.4803485 0.5313677 -0.5452443
[2,] -0.5335421 0.496434 -0.5876518 -1.736094 -0.4803485 0.5313677 -0.5452443
[,93] [,94] [,95] [,96] [,97] [,98] [,99]
[1,] -0.1236524 -0.7788951 -1.171674 1.026973 -0.2723705 -0.8927625 0.5909662
[2,] -0.1236524 -0.7788951 -1.171674 1.026973 -0.2723705 -0.8927625 0.5909662
[,100]
[1,] 0.806602
[2,] 0.806602
>
>
> Max(tmp2)
[1] 2.865757
> Min(tmp2)
[1] -2.301543
> mean(tmp2)
[1] 0.02235029
> Sum(tmp2)
[1] 2.235029
> Var(tmp2)
[1] 0.9134918
>
> rowMeans(tmp2)
[1] -1.03558403 0.20596522 1.53492538 -0.45012848 1.25071805 -0.09102488
[7] -0.30658450 0.63744786 0.66306402 0.36340235 -0.25102660 0.67190891
[13] 2.74734774 -1.46199726 0.08237453 0.77510986 -0.19328548 -0.31976731
[19] 0.62557109 0.10405138 1.11319164 0.30762991 -0.37099154 0.01140859
[25] 0.31547041 1.06271705 0.23765935 -0.09339717 -0.51450445 -1.33117244
[31] -0.12033649 -0.14276461 0.49005122 1.17126356 0.68674730 -0.69913177
[37] -0.16085823 -0.84874701 -0.96060538 -1.61453006 -0.19566262 -0.58151785
[43] -0.80134354 0.42849957 2.86575660 -0.31261514 0.28286212 0.99960923
[49] -1.10982641 -0.01640704 -0.54935963 -0.95813781 0.56226036 1.12039817
[55] 1.30176690 2.02994399 -0.89671306 0.54642237 -1.09796482 0.11454065
[61] 0.47680068 0.24993652 -2.30154292 -0.25704254 0.64540739 -0.04081941
[67] 0.08458503 -1.40174586 0.32197642 0.19731249 0.11485793 1.24475468
[73] -1.38749454 -0.61219939 -0.02722584 1.67465607 0.10813114 -0.38530964
[79] -0.61700928 -0.27448646 -0.50371244 -0.42111588 0.08454661 -0.88398963
[85] 0.03925099 1.09015780 -0.87287624 -1.39839690 1.21681754 1.60486148
[91] -0.92507358 -1.75992602 -0.45016355 0.40073900 0.36193351 -0.25780759
[97] 1.14968674 -2.13288506 -1.15897859 1.41431887
> rowSums(tmp2)
[1] -1.03558403 0.20596522 1.53492538 -0.45012848 1.25071805 -0.09102488
[7] -0.30658450 0.63744786 0.66306402 0.36340235 -0.25102660 0.67190891
[13] 2.74734774 -1.46199726 0.08237453 0.77510986 -0.19328548 -0.31976731
[19] 0.62557109 0.10405138 1.11319164 0.30762991 -0.37099154 0.01140859
[25] 0.31547041 1.06271705 0.23765935 -0.09339717 -0.51450445 -1.33117244
[31] -0.12033649 -0.14276461 0.49005122 1.17126356 0.68674730 -0.69913177
[37] -0.16085823 -0.84874701 -0.96060538 -1.61453006 -0.19566262 -0.58151785
[43] -0.80134354 0.42849957 2.86575660 -0.31261514 0.28286212 0.99960923
[49] -1.10982641 -0.01640704 -0.54935963 -0.95813781 0.56226036 1.12039817
[55] 1.30176690 2.02994399 -0.89671306 0.54642237 -1.09796482 0.11454065
[61] 0.47680068 0.24993652 -2.30154292 -0.25704254 0.64540739 -0.04081941
[67] 0.08458503 -1.40174586 0.32197642 0.19731249 0.11485793 1.24475468
[73] -1.38749454 -0.61219939 -0.02722584 1.67465607 0.10813114 -0.38530964
[79] -0.61700928 -0.27448646 -0.50371244 -0.42111588 0.08454661 -0.88398963
[85] 0.03925099 1.09015780 -0.87287624 -1.39839690 1.21681754 1.60486148
[91] -0.92507358 -1.75992602 -0.45016355 0.40073900 0.36193351 -0.25780759
[97] 1.14968674 -2.13288506 -1.15897859 1.41431887
> 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] -1.03558403 0.20596522 1.53492538 -0.45012848 1.25071805 -0.09102488
[7] -0.30658450 0.63744786 0.66306402 0.36340235 -0.25102660 0.67190891
[13] 2.74734774 -1.46199726 0.08237453 0.77510986 -0.19328548 -0.31976731
[19] 0.62557109 0.10405138 1.11319164 0.30762991 -0.37099154 0.01140859
[25] 0.31547041 1.06271705 0.23765935 -0.09339717 -0.51450445 -1.33117244
[31] -0.12033649 -0.14276461 0.49005122 1.17126356 0.68674730 -0.69913177
[37] -0.16085823 -0.84874701 -0.96060538 -1.61453006 -0.19566262 -0.58151785
[43] -0.80134354 0.42849957 2.86575660 -0.31261514 0.28286212 0.99960923
[49] -1.10982641 -0.01640704 -0.54935963 -0.95813781 0.56226036 1.12039817
[55] 1.30176690 2.02994399 -0.89671306 0.54642237 -1.09796482 0.11454065
[61] 0.47680068 0.24993652 -2.30154292 -0.25704254 0.64540739 -0.04081941
[67] 0.08458503 -1.40174586 0.32197642 0.19731249 0.11485793 1.24475468
[73] -1.38749454 -0.61219939 -0.02722584 1.67465607 0.10813114 -0.38530964
[79] -0.61700928 -0.27448646 -0.50371244 -0.42111588 0.08454661 -0.88398963
[85] 0.03925099 1.09015780 -0.87287624 -1.39839690 1.21681754 1.60486148
[91] -0.92507358 -1.75992602 -0.45016355 0.40073900 0.36193351 -0.25780759
[97] 1.14968674 -2.13288506 -1.15897859 1.41431887
> rowMin(tmp2)
[1] -1.03558403 0.20596522 1.53492538 -0.45012848 1.25071805 -0.09102488
[7] -0.30658450 0.63744786 0.66306402 0.36340235 -0.25102660 0.67190891
[13] 2.74734774 -1.46199726 0.08237453 0.77510986 -0.19328548 -0.31976731
[19] 0.62557109 0.10405138 1.11319164 0.30762991 -0.37099154 0.01140859
[25] 0.31547041 1.06271705 0.23765935 -0.09339717 -0.51450445 -1.33117244
[31] -0.12033649 -0.14276461 0.49005122 1.17126356 0.68674730 -0.69913177
[37] -0.16085823 -0.84874701 -0.96060538 -1.61453006 -0.19566262 -0.58151785
[43] -0.80134354 0.42849957 2.86575660 -0.31261514 0.28286212 0.99960923
[49] -1.10982641 -0.01640704 -0.54935963 -0.95813781 0.56226036 1.12039817
[55] 1.30176690 2.02994399 -0.89671306 0.54642237 -1.09796482 0.11454065
[61] 0.47680068 0.24993652 -2.30154292 -0.25704254 0.64540739 -0.04081941
[67] 0.08458503 -1.40174586 0.32197642 0.19731249 0.11485793 1.24475468
[73] -1.38749454 -0.61219939 -0.02722584 1.67465607 0.10813114 -0.38530964
[79] -0.61700928 -0.27448646 -0.50371244 -0.42111588 0.08454661 -0.88398963
[85] 0.03925099 1.09015780 -0.87287624 -1.39839690 1.21681754 1.60486148
[91] -0.92507358 -1.75992602 -0.45016355 0.40073900 0.36193351 -0.25780759
[97] 1.14968674 -2.13288506 -1.15897859 1.41431887
>
> colMeans(tmp2)
[1] 0.02235029
> colSums(tmp2)
[1] 2.235029
> colVars(tmp2)
[1] 0.9134918
> colSd(tmp2)
[1] 0.9557677
> colMax(tmp2)
[1] 2.865757
> colMin(tmp2)
[1] -2.301543
> colMedians(tmp2)
[1] -0.002499222
> colRanges(tmp2)
[,1]
[1,] -2.301543
[2,] 2.865757
>
> 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] 0.008702694 -3.318735722 -2.755055083 0.647838191 -1.286399630
[6] -1.846142087 5.955649137 3.361755003 1.460780942 -1.720254140
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.9971734
[2,] -0.6386204
[3,] -0.1808481
[4,] 0.6914220
[5,] 2.1765150
>
> rowApply(tmp,sum)
[1] 1.444981125 1.336809954 1.420699872 2.525316728 3.177296833
[6] -1.529877128 -3.262065665 0.002156091 -5.153056285 0.545877781
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 2 4 3 7 7 10 9 10 1 3
[2,] 5 1 7 8 1 3 3 1 7 5
[3,] 6 7 2 2 3 7 4 3 3 10
[4,] 1 6 9 5 9 2 5 5 10 1
[5,] 3 8 4 3 4 9 7 8 6 2
[6,] 10 2 6 4 2 5 8 7 2 6
[7,] 7 9 8 10 5 1 10 9 5 9
[8,] 9 5 10 9 8 4 2 4 8 7
[9,] 8 3 5 6 10 8 6 6 4 8
[10,] 4 10 1 1 6 6 1 2 9 4
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 3.0949205 -0.9861118 -0.9529640 1.2672992 -5.1348263 -1.3971228
[7] -3.2252256 1.9130964 2.9553357 -1.7270841 0.8002593 2.1404711
[13] 2.5334580 -0.5320115 -1.0472503 1.2026761 -6.1105330 -0.8586222
[19] 1.9534709 -0.6406070
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.2455096
[2,] 0.4342762
[3,] 0.6902848
[4,] 1.3602720
[5,] 1.8555972
>
> rowApply(tmp,sum)
[1] -4.9446588 -0.3194314 -1.6147972 1.1254258 1.0020901
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 2 19 15 18 15
[2,] 15 6 19 6 6
[3,] 19 8 10 5 13
[4,] 6 20 17 7 12
[5,] 16 1 2 2 5
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -1.2455096 0.1500106 0.6435281 -0.5909837 0.2230699 -0.4678923
[2,] 1.8555972 -0.8475642 -0.7826155 1.9280204 -2.3246981 -0.6603544
[3,] 0.4342762 0.9732571 -0.1646095 0.7396696 -1.1070100 -1.3791507
[4,] 1.3602720 -0.7209947 -0.8655559 -0.6489965 -1.2179951 1.9249197
[5,] 0.6902848 -0.5408207 0.2162888 -0.1604107 -0.7081930 -0.8146450
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.4529500 -0.06175271 -0.1869275 -1.0092697 -0.87146121 0.08439741
[2,] -1.4543481 -0.92239481 1.2237735 0.3188559 0.99042510 0.68484835
[3,] 0.1241003 -0.99191537 -0.4058879 -0.3269486 1.27982082 0.95463757
[4,] -1.1100591 1.43027139 1.0887330 0.1643946 -0.08503835 -0.33357658
[5,] -0.3319689 2.45888793 1.2356446 -0.8741162 -0.51348708 0.75016432
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 0.1245317 0.28240053 -0.1750563 -0.8640775 -2.54582674 0.5596818
[2,] 1.3853100 -0.41017244 -1.4529582 1.2361054 -1.30359856 0.4050608
[3,] -0.8266578 0.08617982 0.6265652 -1.0132974 -0.05875888 -0.6889474
[4,] 1.1356420 -0.11579246 -0.5958081 0.6763128 -1.33506324 -0.8813273
[5,] 0.7146320 -0.37462694 0.5500071 1.1676328 -0.86728553 -0.2530900
[,19] [,20]
[1,] 0.005379413 1.4540489
[2,] 0.640550199 -0.8292740
[3,] 0.403853433 -0.2739737
[4,] 1.069654080 0.1854337
[5,] -0.165966192 -1.1768419
>
>
> 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 : 654 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 : 565 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 -0.1789235 2.212946 -0.5389274 -0.2541402 -1.528169 -0.4246237 -0.3162535
col8 col9 col10 col11 col12 col13 col14
row1 -0.2101173 -0.2017926 -0.04152432 1.921044 0.5233035 0.9422542 -0.7579342
col15 col16 col17 col18 col19 col20
row1 1.516494 0.2790274 0.4840719 -0.37677 -0.4710194 -1.107585
> tmp[,"col10"]
col10
row1 -0.041524319
row2 -0.008814091
row3 -0.105544567
row4 0.054047948
row5 1.029360115
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 -0.1789235 2.2129464 -0.5389274 -0.2541402 -1.528169 -0.4246237 -0.3162535
row5 -1.4146737 0.2936669 1.7446788 1.6490549 1.649333 0.9358355 2.4523483
col8 col9 col10 col11 col12 col13 col14
row1 -0.2101173 -0.2017926 -0.04152432 1.9210437 0.5233035 0.9422542 -0.7579342
row5 -1.0611681 -0.2662734 1.02936011 0.2674379 0.5346530 0.1937207 -0.7357845
col15 col16 col17 col18 col19 col20
row1 1.5164939 0.2790274 0.4840719 -0.3767700 -0.4710194 -1.1075854
row5 0.6037376 1.4610031 0.5851351 0.6430044 -1.1067184 0.4943234
> tmp[,c("col6","col20")]
col6 col20
row1 -0.4246237 -1.1075854
row2 0.8697776 2.5762897
row3 -2.0317085 -0.6608429
row4 1.8777694 -0.8041603
row5 0.9358355 0.4943234
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -0.4246237 -1.1075854
row5 0.9358355 0.4943234
>
>
>
>
> 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 49.85814 51.18613 48.32309 51.15126 50.44426 104.9249 49.66283 48.24967
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.56264 49.9988 50.8038 51.03135 48.49098 51.63333 49.90631 48.1687
col17 col18 col19 col20
row1 49.08301 51.32946 51.77614 105.4764
> tmp[,"col10"]
col10
row1 49.99880
row2 30.03577
row3 30.31442
row4 30.88143
row5 48.87341
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.85814 51.18613 48.32309 51.15126 50.44426 104.9249 49.66283 48.24967
row5 49.94086 49.29555 49.44871 49.06960 48.43162 105.7035 50.94724 49.43549
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.56264 49.99880 50.80380 51.03135 48.49098 51.63333 49.90631 48.16870
row5 46.06681 48.87341 48.72956 49.82995 50.44587 49.53988 49.21371 50.14748
col17 col18 col19 col20
row1 49.08301 51.32946 51.77614 105.4764
row5 48.73365 52.13800 49.07587 105.0798
> tmp[,c("col6","col20")]
col6 col20
row1 104.92487 105.47640
row2 77.55360 74.36938
row3 75.18914 74.45824
row4 75.17026 75.82354
row5 105.70352 105.07978
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 104.9249 105.4764
row5 105.7035 105.0798
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 104.9249 105.4764
row5 105.7035 105.0798
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 1.11157639
[2,] 0.67564557
[3,] 1.15985803
[4,] -0.05474541
[5,] -0.85292182
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.5950998 -2.2025887
[2,] -0.1813552 -0.6556627
[3,] 0.7884217 0.3404709
[4,] -0.3102787 -0.3618552
[5,] -0.9244021 -1.1968648
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.2539444 -0.1935172
[2,] -0.6532572 0.1696251
[3,] -1.0087317 0.2730454
[4,] -1.5919698 -0.1542890
[5,] 0.7187234 0.5640201
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.2539444
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.2539444
[2,] -0.6532572
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6]
row3 0.3557772 -3.2488332 -1.8606487 0.5303121 0.9893872 -0.6361222
row1 1.1040385 0.6472939 -0.5076686 -0.4090557 -1.3477808 -1.0126701
[,7] [,8] [,9] [,10] [,11] [,12]
row3 0.5357493 -0.07727854 -0.2735377 -2.5452606 0.2995434 0.1498301
row1 -1.1986606 0.21038442 -0.5918738 0.6412233 1.4902154 -0.6350544
[,13] [,14] [,15] [,16] [,17] [,18] [,19]
row3 0.79156314 -0.6921589 0.2762742 -0.9653936 -0.4617592 -1.186426 0.7038837
row1 0.09396183 0.1203837 -1.0881514 -1.7822163 0.7289607 1.212941 0.6094237
[,20]
row3 2.2199805
row1 0.3931711
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -1.615302 1.369232 0.3269146 -0.8400764 -1.251736 0.4472758 1.233577
[,8] [,9] [,10]
row2 -0.1911981 1.135517 0.8977976
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6]
row5 -0.6119451 -0.1332143 -0.009352267 0.5025394 -0.02479248 0.6190556
[,7] [,8] [,9] [,10] [,11] [,12] [,13]
row5 0.3016655 -0.5966292 -0.3249371 0.664261 1.064151 0.4665376 -0.1375478
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row5 -1.983498 0.8447154 -0.784947 -1.474001 0.1261001 -1.191851 0.7449394
>
>
> 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: 0x6402609a4b70>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c6f8258a72c3f"
[2] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c6f82163c314b"
[3] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c6f823c4a6959"
[4] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c6f8243d8897f"
[5] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c6f82a83655a"
[6] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c6f8257b2f20f"
[7] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c6f8213c691a2"
[8] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c6f82680d3a79"
[9] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c6f824d557edc"
[10] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c6f82470e5d98"
[11] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c6f826d8c2fc9"
[12] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c6f82292049e9"
[13] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c6f825453756f"
[14] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c6f8244fac3fa"
[15] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1c6f822215ee16"
>
>
> ### 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: 0x6402612bdd00>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x6402612bdd00>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x6402612bdd00>
> rowMedians(tmp)
[1] 0.257406123 -0.248467262 0.434446232 0.252855116 0.048861575
[6] 0.262956718 -0.099574662 -0.357654407 -0.198867912 -0.062476880
[11] -0.206573075 0.222229912 -0.275967425 0.783386486 0.203202038
[16] -0.404035747 -0.033497406 -0.196115980 -0.021229097 -0.303344566
[21] 0.271247574 -0.741423622 0.046028486 0.326336715 -0.076099066
[26] -0.604106148 -0.322718770 -0.230961007 -0.225737280 -0.285736759
[31] 0.169445556 -0.531879622 -0.398157256 0.072628543 0.366898614
[36] 0.023281384 -0.195526575 0.058430249 0.051607777 -0.145364088
[41] -0.062110646 -0.214772492 0.417684197 0.029171249 0.106976484
[46] -0.045345804 -0.430696124 0.023262285 -0.108348137 0.428654265
[51] 0.295276453 0.227449310 -0.179256399 -0.088296670 -0.272917610
[56] -0.140487808 -0.108372202 0.426315535 -0.045616530 -0.432965354
[61] -0.421165531 -0.290990055 -0.558994695 -0.318082222 -0.398771997
[66] -0.089056472 -0.172779130 -0.370119803 0.185407104 -0.163606342
[71] 0.179790856 0.550281471 -0.146560625 -0.179040931 0.094068245
[76] 0.172286852 -0.202794766 -0.061130131 -0.516667297 -0.032128866
[81] 0.338340440 0.129160926 -0.099633000 0.428078469 -0.097860528
[86] 0.126904499 0.260622677 0.225660385 -0.141775341 0.227762377
[91] 0.019322506 -0.272279103 0.195559740 -0.149703013 0.004746327
[96] 0.068157353 -0.170526125 0.304902884 -0.297143525 0.348272252
[101] 0.034791224 0.308262972 0.051391366 0.226803133 -0.008161678
[106] -0.190268886 0.441379341 0.660443556 -0.438309333 -0.227670791
[111] -0.314692112 0.156857930 -0.702115118 -0.181403127 -0.380428001
[116] -0.118185927 -0.206623690 -0.082598673 1.023408790 0.119161918
[121] 0.529273841 0.014242246 0.047931047 1.059607542 0.053981428
[126] -0.199429197 -0.075172962 0.024929573 0.251483279 0.294319204
[131] -0.162619070 0.147572653 -0.107538004 0.007618277 -0.387613188
[136] -0.107479682 0.061208448 -0.465698110 -0.363371214 -0.477380911
[141] -0.003088290 0.115138728 -0.031087219 -0.239329320 -0.070391474
[146] -0.205201291 -0.176775581 0.208472525 -0.450605710 0.683307794
[151] -0.359005798 -0.017628892 -0.183239002 -0.237527359 0.219783894
[156] 0.255265386 0.113402045 0.334400558 -0.452613899 0.203292655
[161] 0.063525694 -0.097954876 -0.127488385 -0.028399450 -0.004561943
[166] -0.066924166 0.670876238 0.413225595 0.520076820 0.242430349
[171] 0.017665361 -0.199765863 0.163881648 0.078446611 -0.084085142
[176] -0.132858417 0.367730446 0.038927364 0.157758054 0.330578308
[181] 0.296219724 0.004709964 -0.139719123 0.409055543 -0.337748776
[186] -0.244783095 -0.585574720 -0.047502417 -0.191821314 0.005840437
[191] -0.303080940 -0.233435151 -0.855657356 0.119818718 -0.210765603
[196] 0.607636180 -0.142198581 0.435523723 0.365657073 0.205944303
[201] 0.025332773 0.175502555 -0.622509684 -0.144494329 0.167289469
[206] -0.632963999 0.394738966 -0.140800095 -0.033457593 0.426458010
[211] 0.119773441 0.266435553 0.099786020 -0.369180387 -0.264160459
[216] 0.051304010 -0.414600824 -0.660642485 -0.359879493 -0.534812933
[221] -0.308914118 0.125856631 -0.408348277 -0.025358281 -0.136190233
[226] -0.565682366 0.069136555 -0.366700529 0.079021912 -0.477087911
>
> proc.time()
user system elapsed
1.222 0.656 1.866
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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: 0x58d4851dd370>
> .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: 0x58d4851dd370>
> .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: 0x58d4851dd370>
> .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: 0x58d4851dd370>
> 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: 0x58d4851c51c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x58d4851c51c0>
> .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: 0x58d4851c51c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x58d4851c51c0>
> .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: 0x58d4851c51c0>
> 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: 0x58d4854a8120>
> .Call("R_bm_AddColumn",P)
<pointer: 0x58d4854a8120>
> .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: 0x58d4854a8120>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x58d4854a8120>
> .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: 0x58d4854a8120>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x58d4854a8120>
> .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: 0x58d4854a8120>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x58d4854a8120>
> .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: 0x58d4854a8120>
> 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: 0x58d4841f8390>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x58d4841f8390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x58d4841f8390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x58d4841f8390>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile1c735b289fbd46" "BufferedMatrixFile1c735b2a1ae68c"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile1c735b289fbd46" "BufferedMatrixFile1c735b2a1ae68c"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x58d4840ef3d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x58d4840ef3d0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x58d4840ef3d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x58d4840ef3d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x58d4840ef3d0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x58d4840ef3d0>
> .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: 0x58d485c24fa0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x58d485c24fa0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x58d485c24fa0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x58d485c24fa0>
> 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: 0x58d4843fcff0>
> .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: 0x58d4843fcff0>
> rm(P)
>
> proc.time()
user system elapsed
0.253 0.040 0.280
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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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
0.252 0.046 0.285