Ben Bolstad
| Snapshot Date: 2026-03-15 13:40 -0400 (Sun, 15 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: devel |
| git_last_commit: ecdbf23 |
| git_last_commit_date: 2025-10-29 09:58:55 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-16 11:33 -0400 (Mon, 16 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4837 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 4053 |
| 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 256/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.75.0 (landing page) Ben Bolstad
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
| 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: 1.75.0 |
| 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_1.75.0.tar.gz |
| StartedAt: 2026-03-15 22:34:14 -0400 (Sun, 15 Mar 2026) |
| EndedAt: 2026-03-15 22:34:39 -0400 (Sun, 15 Mar 2026) |
| EllapsedTime: 25.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.75.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-16 02:34:15 UTC
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.75.0’
* 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
##############################################################################
##############################################################################
###
### 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 ‘1.75.0’
** 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 Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
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
0.229 0.056 0.274
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
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 479482 25.7 1050322 56.1 639251 34.2
Vcells 886403 6.8 8388608 64.0 2083267 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] "Sun Mar 15 22:34:29 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] "Sun Mar 15 22:34:29 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: 0x6155d9ff2ff0>
>
>
>
> 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] "Sun Mar 15 22:34:30 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] "Sun Mar 15 22:34:30 2026"
>
> ColMode(tmp2)
<pointer: 0x6155d9ff2ff0>
>
>
>
> ### 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,] 99.7276543 1.38685583 0.88807496 -1.5128544
[2,] -0.2066953 -0.03782833 1.08933902 -0.4850682
[3,] -0.3676730 -1.04793493 -1.39263107 -0.1334299
[4,] -0.4427473 1.22540803 -0.01245285 -0.3403574
> 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 : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 99.7276543 1.38685583 0.88807496 1.5128544
[2,] 0.2066953 0.03782833 1.08933902 0.4850682
[3,] 0.3676730 1.04793493 1.39263107 0.1334299
[4,] 0.4427473 1.22540803 0.01245285 0.3403574
> 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 : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 9.9863734 1.1776484 0.9423773 1.2299814
[2,] 0.4546375 0.1944951 1.0437141 0.6964684
[3,] 0.6063605 1.0236869 1.1800979 0.3652806
[4,] 0.6653926 1.1069815 0.1115923 0.5834016
>
> 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 : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 224.59139 38.16334 35.31185 38.81267
[2,] 29.75307 26.98278 36.52648 32.44975
[3,] 31.43128 36.28480 38.19361 28.78624
[4,] 32.09667 37.29522 26.12838 31.17437
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x6155d99d9560>
> exp(tmp5)
<pointer: 0x6155d99d9560>
> log(tmp5,2)
<pointer: 0x6155d99d9560>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 467.4575
> Min(tmp5)
[1] 53.08006
> mean(tmp5)
[1] 72.56833
> Sum(tmp5)
[1] 14513.67
> Var(tmp5)
[1] 853.9482
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 90.81907 66.77282 69.91715 70.99570 71.11408 70.70138 73.15121 68.71881
[9] 72.02254 71.47055
> rowSums(tmp5)
[1] 1816.381 1335.456 1398.343 1419.914 1422.282 1414.028 1463.024 1374.376
[9] 1440.451 1429.411
> rowVars(tmp5)
[1] 7959.09509 65.81258 68.35994 58.04926 72.28759 55.63626
[7] 55.33688 40.27864 55.52471 94.19093
> rowSd(tmp5)
[1] 89.213761 8.112495 8.268007 7.619006 8.502211 7.458972 7.438876
[8] 6.346545 7.451491 9.705201
> rowMax(tmp5)
[1] 467.45755 84.45046 87.20193 82.06908 85.20043 82.44701 80.11539
[8] 80.49794 85.09464 91.35836
> rowMin(tmp5)
[1] 53.48222 55.70379 57.63116 54.38279 54.44066 53.08006 54.91202 58.43361
[9] 55.42649 55.50954
>
> colMeans(tmp5)
[1] 106.03433 72.93621 75.69807 71.50650 66.90210 66.77740 67.19582
[8] 70.85783 71.60345 69.87773 70.08188 74.74581 72.13830 71.04528
[15] 68.52385 71.32636 69.78830 69.89415 72.71034 71.72295
> colSums(tmp5)
[1] 1060.3433 729.3621 756.9807 715.0650 669.0210 667.7740 671.9582
[8] 708.5783 716.0345 698.7773 700.8188 747.4581 721.3830 710.4528
[15] 685.2385 713.2636 697.8830 698.9415 727.1034 717.2295
> colVars(tmp5)
[1] 16163.87096 60.99123 63.69674 49.39725 76.52359 90.07902
[7] 48.27667 113.08631 38.02077 23.99011 60.05461 87.93825
[13] 64.11085 84.54939 56.99876 148.53117 75.94091 44.25780
[19] 26.24119 78.99265
> colSd(tmp5)
[1] 127.137213 7.809688 7.981024 7.028318 8.747776 9.490997
[7] 6.948141 10.634205 6.166099 4.897970 7.749491 9.377540
[13] 8.006925 9.195074 7.549752 12.187336 8.714408 6.652653
[19] 5.122615 8.887781
> colMax(tmp5)
[1] 467.45755 79.72073 82.44701 80.78348 80.49794 83.06444 77.36545
[8] 85.09464 79.87883 78.74012 81.09957 87.20193 85.20043 87.28196
[15] 83.10832 91.35836 82.06908 78.35922 83.16632 88.45055
> colMin(tmp5)
[1] 54.44066 56.16112 54.38279 59.91478 53.48222 53.65418 56.87650 55.50954
[9] 60.20343 62.98212 55.42649 60.72514 58.43361 58.26624 54.91202 53.08006
[17] 56.86693 59.73215 67.74440 60.34270
>
>
> ### setting a random element to NA and then testing with na.rm=TRUE or na.rm=FALSE (The default)
>
>
> which.row <- sample(1:10,1,replace=TRUE)
> which.col <- sample(1:20,1,replace=TRUE)
>
> tmp5[which.row,which.col] <- NA
>
> Max(tmp5)
[1] NA
> Min(tmp5)
[1] NA
> mean(tmp5)
[1] NA
> Sum(tmp5)
[1] NA
> Var(tmp5)
[1] NA
>
> rowMeans(tmp5)
[1] 90.81907 66.77282 NA 70.99570 71.11408 70.70138 73.15121 68.71881
[9] 72.02254 71.47055
> rowSums(tmp5)
[1] 1816.381 1335.456 NA 1419.914 1422.282 1414.028 1463.024 1374.376
[9] 1440.451 1429.411
> rowVars(tmp5)
[1] 7959.09509 65.81258 66.79308 58.04926 72.28759 55.63626
[7] 55.33688 40.27864 55.52471 94.19093
> rowSd(tmp5)
[1] 89.213761 8.112495 8.172703 7.619006 8.502211 7.458972 7.438876
[8] 6.346545 7.451491 9.705201
> rowMax(tmp5)
[1] 467.45755 84.45046 NA 82.06908 85.20043 82.44701 80.11539
[8] 80.49794 85.09464 91.35836
> rowMin(tmp5)
[1] 53.48222 55.70379 NA 54.38279 54.44066 53.08006 54.91202 58.43361
[9] 55.42649 55.50954
>
> colMeans(tmp5)
[1] 106.03433 72.93621 NA 71.50650 66.90210 66.77740 67.19582
[8] 70.85783 71.60345 69.87773 70.08188 74.74581 72.13830 71.04528
[15] 68.52385 71.32636 69.78830 69.89415 72.71034 71.72295
> colSums(tmp5)
[1] 1060.3433 729.3621 NA 715.0650 669.0210 667.7740 671.9582
[8] 708.5783 716.0345 698.7773 700.8188 747.4581 721.3830 710.4528
[15] 685.2385 713.2636 697.8830 698.9415 727.1034 717.2295
> colVars(tmp5)
[1] 16163.87096 60.99123 NA 49.39725 76.52359 90.07902
[7] 48.27667 113.08631 38.02077 23.99011 60.05461 87.93825
[13] 64.11085 84.54939 56.99876 148.53117 75.94091 44.25780
[19] 26.24119 78.99265
> colSd(tmp5)
[1] 127.137213 7.809688 NA 7.028318 8.747776 9.490997
[7] 6.948141 10.634205 6.166099 4.897970 7.749491 9.377540
[13] 8.006925 9.195074 7.549752 12.187336 8.714408 6.652653
[19] 5.122615 8.887781
> colMax(tmp5)
[1] 467.45755 79.72073 NA 80.78348 80.49794 83.06444 77.36545
[8] 85.09464 79.87883 78.74012 81.09957 87.20193 85.20043 87.28196
[15] 83.10832 91.35836 82.06908 78.35922 83.16632 88.45055
> colMin(tmp5)
[1] 54.44066 56.16112 NA 59.91478 53.48222 53.65418 56.87650 55.50954
[9] 60.20343 62.98212 55.42649 60.72514 58.43361 58.26624 54.91202 53.08006
[17] 56.86693 59.73215 67.74440 60.34270
>
> Max(tmp5,na.rm=TRUE)
[1] 467.4575
> Min(tmp5,na.rm=TRUE)
[1] 53.08006
> mean(tmp5,na.rm=TRUE)
[1] 72.53353
> Sum(tmp5,na.rm=TRUE)
[1] 14434.17
> Var(tmp5,na.rm=TRUE)
[1] 858.0175
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.81907 66.77282 69.41305 70.99570 71.11408 70.70138 73.15121 68.71881
[9] 72.02254 71.47055
> rowSums(tmp5,na.rm=TRUE)
[1] 1816.381 1335.456 1318.848 1419.914 1422.282 1414.028 1463.024 1374.376
[9] 1440.451 1429.411
> rowVars(tmp5,na.rm=TRUE)
[1] 7959.09509 65.81258 66.79308 58.04926 72.28759 55.63626
[7] 55.33688 40.27864 55.52471 94.19093
> rowSd(tmp5,na.rm=TRUE)
[1] 89.213761 8.112495 8.172703 7.619006 8.502211 7.458972 7.438876
[8] 6.346545 7.451491 9.705201
> rowMax(tmp5,na.rm=TRUE)
[1] 467.45755 84.45046 87.20193 82.06908 85.20043 82.44701 80.11539
[8] 80.49794 85.09464 91.35836
> rowMin(tmp5,na.rm=TRUE)
[1] 53.48222 55.70379 57.63116 54.38279 54.44066 53.08006 54.91202 58.43361
[9] 55.42649 55.50954
>
> colMeans(tmp5,na.rm=TRUE)
[1] 106.03433 72.93621 75.27619 71.50650 66.90210 66.77740 67.19582
[8] 70.85783 71.60345 69.87773 70.08188 74.74581 72.13830 71.04528
[15] 68.52385 71.32636 69.78830 69.89415 72.71034 71.72295
> colSums(tmp5,na.rm=TRUE)
[1] 1060.3433 729.3621 677.4857 715.0650 669.0210 667.7740 671.9582
[8] 708.5783 716.0345 698.7773 700.8188 747.4581 721.3830 710.4528
[15] 685.2385 713.2636 697.8830 698.9415 727.1034 717.2295
> colVars(tmp5,na.rm=TRUE)
[1] 16163.87096 60.99123 69.65652 49.39725 76.52359 90.07902
[7] 48.27667 113.08631 38.02077 23.99011 60.05461 87.93825
[13] 64.11085 84.54939 56.99876 148.53117 75.94091 44.25780
[19] 26.24119 78.99265
> colSd(tmp5,na.rm=TRUE)
[1] 127.137213 7.809688 8.346048 7.028318 8.747776 9.490997
[7] 6.948141 10.634205 6.166099 4.897970 7.749491 9.377540
[13] 8.006925 9.195074 7.549752 12.187336 8.714408 6.652653
[19] 5.122615 8.887781
> colMax(tmp5,na.rm=TRUE)
[1] 467.45755 79.72073 82.44701 80.78348 80.49794 83.06444 77.36545
[8] 85.09464 79.87883 78.74012 81.09957 87.20193 85.20043 87.28196
[15] 83.10832 91.35836 82.06908 78.35922 83.16632 88.45055
> colMin(tmp5,na.rm=TRUE)
[1] 54.44066 56.16112 54.38279 59.91478 53.48222 53.65418 56.87650 55.50954
[9] 60.20343 62.98212 55.42649 60.72514 58.43361 58.26624 54.91202 53.08006
[17] 56.86693 59.73215 67.74440 60.34270
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.81907 66.77282 NaN 70.99570 71.11408 70.70138 73.15121 68.71881
[9] 72.02254 71.47055
> rowSums(tmp5,na.rm=TRUE)
[1] 1816.381 1335.456 0.000 1419.914 1422.282 1414.028 1463.024 1374.376
[9] 1440.451 1429.411
> rowVars(tmp5,na.rm=TRUE)
[1] 7959.09509 65.81258 NA 58.04926 72.28759 55.63626
[7] 55.33688 40.27864 55.52471 94.19093
> rowSd(tmp5,na.rm=TRUE)
[1] 89.213761 8.112495 NA 7.619006 8.502211 7.458972 7.438876
[8] 6.346545 7.451491 9.705201
> rowMax(tmp5,na.rm=TRUE)
[1] 467.45755 84.45046 NA 82.06908 85.20043 82.44701 80.11539
[8] 80.49794 85.09464 91.35836
> rowMin(tmp5,na.rm=TRUE)
[1] 53.48222 55.70379 NA 54.38279 54.44066 53.08006 54.91202 58.43361
[9] 55.42649 55.50954
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 110.54702 72.64890 NaN 72.79447 67.85758 64.96772 67.27360
[8] 71.20638 71.44558 69.88764 70.33787 73.36180 72.12667 71.92352
[15] 68.49814 70.35869 71.13910 69.38667 73.26211 72.95854
> colSums(tmp5,na.rm=TRUE)
[1] 994.9232 653.8401 0.0000 655.1502 610.7182 584.7095 605.4624 640.8574
[9] 643.0103 628.9887 633.0408 660.2562 649.1400 647.3117 616.4833 633.2282
[17] 640.2519 624.4801 659.3590 656.6268
> colVars(tmp5,na.rm=TRUE)
[1] 17955.25528 67.68643 NA 36.90969 75.81836 64.49613
[7] 54.24319 125.85539 42.49299 26.98777 66.82421 77.38123
[13] 72.12319 86.44081 64.11616 156.56314 64.90627 46.89277
[19] 26.09626 71.69147
> colSd(tmp5,na.rm=TRUE)
[1] 133.997221 8.227177 NA 6.075334 8.707374 8.030948
[7] 7.364998 11.218529 6.518665 5.194975 8.174608 8.796660
[13] 8.492537 9.297355 8.007257 12.512520 8.056443 6.847829
[19] 5.108450 8.467082
> colMax(tmp5,na.rm=TRUE)
[1] 467.45755 79.72073 -Inf 80.78348 80.49794 74.39379 77.36545
[8] 85.09464 79.87883 78.74012 81.09957 84.45046 85.20043 87.28196
[15] 83.10832 91.35836 82.06908 78.35922 83.16632 88.45055
> colMin(tmp5,na.rm=TRUE)
[1] 54.44066 56.16112 Inf 64.88537 53.48222 53.65418 56.87650 55.50954
[9] 60.20343 62.98212 55.42649 60.72514 58.43361 58.26624 54.91202 53.08006
[17] 56.86693 59.73215 69.05156 60.34270
>
>
>
>
> 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] 202.4599 257.9731 318.2340 196.4542 164.7265 239.0709 152.6185 323.4194
[9] 197.9298 176.0219
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 202.4599 257.9731 318.2340 196.4542 164.7265 239.0709 152.6185 323.4194
[9] 197.9298 176.0219
>
>
>
> 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] 2.842171e-14 0.000000e+00 -5.684342e-14 5.684342e-14 1.705303e-13
[6] -2.842171e-14 4.263256e-14 2.842171e-14 1.421085e-13 0.000000e+00
[11] -5.684342e-14 -2.842171e-14 -2.842171e-14 -1.136868e-13 0.000000e+00
[16] -8.526513e-14 0.000000e+00 0.000000e+00 7.105427e-14 7.105427e-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)
+ }
2 4
3 20
5 19
8 5
8 18
8 8
6 4
8 19
1 6
3 19
4 13
3 5
8 15
4 4
4 7
7 11
2 13
1 4
3 9
10 7
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] 2.085111
> Min(tmp)
[1] -2.35551
> mean(tmp)
[1] -0.283236
> Sum(tmp)
[1] -28.3236
> Var(tmp)
[1] 0.9175418
>
> rowMeans(tmp)
[1] -0.283236
> rowSums(tmp)
[1] -28.3236
> rowVars(tmp)
[1] 0.9175418
> rowSd(tmp)
[1] 0.957884
> rowMax(tmp)
[1] 2.085111
> rowMin(tmp)
[1] -2.35551
>
> colMeans(tmp)
[1] -0.85804540 -0.68582384 1.47840369 -0.38462543 -1.08264282 -0.25381910
[7] -0.03840864 0.43204946 -1.95062604 -0.36543847 -0.12962345 -0.77193399
[13] 0.56984434 -1.63313225 -0.72460768 -1.63275161 -1.14065941 -1.09309069
[19] -1.80483333 1.46041483 -0.78766576 0.54021694 0.82223145 0.18473436
[25] -1.90523714 0.58877440 -0.38728403 -0.44177993 -1.67340527 0.68930325
[31] 0.96110045 -0.13456023 0.52096092 0.22599886 0.13369532 -0.15341746
[37] -1.20318216 -0.55135865 -2.14240706 0.53562415 -1.34381031 0.68866629
[43] -0.12595512 0.87262330 -0.34777501 -2.04723082 -0.34636989 -2.07148363
[49] -2.35551047 -1.81690506 -0.92111044 -0.54687084 -1.37454708 1.04827270
[55] -0.70978934 -0.17212625 0.85218953 -0.95259330 -1.66392563 0.25761261
[61] -0.57133022 0.34770256 -0.17881049 0.16044804 -1.30481497 0.55937758
[67] 0.19757804 -0.65513603 0.57528962 -1.55201811 0.58806527 -0.18124386
[73] 0.11128344 -0.44191918 1.40177110 -0.68171644 2.08511103 0.07637645
[79] -0.58957677 -1.28548694 0.49805599 0.15064732 -1.29405226 -0.69274424
[85] 0.16011624 -0.77280163 0.52660980 1.71723995 -0.29966627 0.22712113
[91] -0.66271943 1.33134109 0.46419295 -0.06668299 1.63273817 0.13662994
[97] -0.07695526 -0.54742458 -1.10144068 -0.45110518
> colSums(tmp)
[1] -0.85804540 -0.68582384 1.47840369 -0.38462543 -1.08264282 -0.25381910
[7] -0.03840864 0.43204946 -1.95062604 -0.36543847 -0.12962345 -0.77193399
[13] 0.56984434 -1.63313225 -0.72460768 -1.63275161 -1.14065941 -1.09309069
[19] -1.80483333 1.46041483 -0.78766576 0.54021694 0.82223145 0.18473436
[25] -1.90523714 0.58877440 -0.38728403 -0.44177993 -1.67340527 0.68930325
[31] 0.96110045 -0.13456023 0.52096092 0.22599886 0.13369532 -0.15341746
[37] -1.20318216 -0.55135865 -2.14240706 0.53562415 -1.34381031 0.68866629
[43] -0.12595512 0.87262330 -0.34777501 -2.04723082 -0.34636989 -2.07148363
[49] -2.35551047 -1.81690506 -0.92111044 -0.54687084 -1.37454708 1.04827270
[55] -0.70978934 -0.17212625 0.85218953 -0.95259330 -1.66392563 0.25761261
[61] -0.57133022 0.34770256 -0.17881049 0.16044804 -1.30481497 0.55937758
[67] 0.19757804 -0.65513603 0.57528962 -1.55201811 0.58806527 -0.18124386
[73] 0.11128344 -0.44191918 1.40177110 -0.68171644 2.08511103 0.07637645
[79] -0.58957677 -1.28548694 0.49805599 0.15064732 -1.29405226 -0.69274424
[85] 0.16011624 -0.77280163 0.52660980 1.71723995 -0.29966627 0.22712113
[91] -0.66271943 1.33134109 0.46419295 -0.06668299 1.63273817 0.13662994
[97] -0.07695526 -0.54742458 -1.10144068 -0.45110518
> 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] -0.85804540 -0.68582384 1.47840369 -0.38462543 -1.08264282 -0.25381910
[7] -0.03840864 0.43204946 -1.95062604 -0.36543847 -0.12962345 -0.77193399
[13] 0.56984434 -1.63313225 -0.72460768 -1.63275161 -1.14065941 -1.09309069
[19] -1.80483333 1.46041483 -0.78766576 0.54021694 0.82223145 0.18473436
[25] -1.90523714 0.58877440 -0.38728403 -0.44177993 -1.67340527 0.68930325
[31] 0.96110045 -0.13456023 0.52096092 0.22599886 0.13369532 -0.15341746
[37] -1.20318216 -0.55135865 -2.14240706 0.53562415 -1.34381031 0.68866629
[43] -0.12595512 0.87262330 -0.34777501 -2.04723082 -0.34636989 -2.07148363
[49] -2.35551047 -1.81690506 -0.92111044 -0.54687084 -1.37454708 1.04827270
[55] -0.70978934 -0.17212625 0.85218953 -0.95259330 -1.66392563 0.25761261
[61] -0.57133022 0.34770256 -0.17881049 0.16044804 -1.30481497 0.55937758
[67] 0.19757804 -0.65513603 0.57528962 -1.55201811 0.58806527 -0.18124386
[73] 0.11128344 -0.44191918 1.40177110 -0.68171644 2.08511103 0.07637645
[79] -0.58957677 -1.28548694 0.49805599 0.15064732 -1.29405226 -0.69274424
[85] 0.16011624 -0.77280163 0.52660980 1.71723995 -0.29966627 0.22712113
[91] -0.66271943 1.33134109 0.46419295 -0.06668299 1.63273817 0.13662994
[97] -0.07695526 -0.54742458 -1.10144068 -0.45110518
> colMin(tmp)
[1] -0.85804540 -0.68582384 1.47840369 -0.38462543 -1.08264282 -0.25381910
[7] -0.03840864 0.43204946 -1.95062604 -0.36543847 -0.12962345 -0.77193399
[13] 0.56984434 -1.63313225 -0.72460768 -1.63275161 -1.14065941 -1.09309069
[19] -1.80483333 1.46041483 -0.78766576 0.54021694 0.82223145 0.18473436
[25] -1.90523714 0.58877440 -0.38728403 -0.44177993 -1.67340527 0.68930325
[31] 0.96110045 -0.13456023 0.52096092 0.22599886 0.13369532 -0.15341746
[37] -1.20318216 -0.55135865 -2.14240706 0.53562415 -1.34381031 0.68866629
[43] -0.12595512 0.87262330 -0.34777501 -2.04723082 -0.34636989 -2.07148363
[49] -2.35551047 -1.81690506 -0.92111044 -0.54687084 -1.37454708 1.04827270
[55] -0.70978934 -0.17212625 0.85218953 -0.95259330 -1.66392563 0.25761261
[61] -0.57133022 0.34770256 -0.17881049 0.16044804 -1.30481497 0.55937758
[67] 0.19757804 -0.65513603 0.57528962 -1.55201811 0.58806527 -0.18124386
[73] 0.11128344 -0.44191918 1.40177110 -0.68171644 2.08511103 0.07637645
[79] -0.58957677 -1.28548694 0.49805599 0.15064732 -1.29405226 -0.69274424
[85] 0.16011624 -0.77280163 0.52660980 1.71723995 -0.29966627 0.22712113
[91] -0.66271943 1.33134109 0.46419295 -0.06668299 1.63273817 0.13662994
[97] -0.07695526 -0.54742458 -1.10144068 -0.45110518
> colMedians(tmp)
[1] -0.85804540 -0.68582384 1.47840369 -0.38462543 -1.08264282 -0.25381910
[7] -0.03840864 0.43204946 -1.95062604 -0.36543847 -0.12962345 -0.77193399
[13] 0.56984434 -1.63313225 -0.72460768 -1.63275161 -1.14065941 -1.09309069
[19] -1.80483333 1.46041483 -0.78766576 0.54021694 0.82223145 0.18473436
[25] -1.90523714 0.58877440 -0.38728403 -0.44177993 -1.67340527 0.68930325
[31] 0.96110045 -0.13456023 0.52096092 0.22599886 0.13369532 -0.15341746
[37] -1.20318216 -0.55135865 -2.14240706 0.53562415 -1.34381031 0.68866629
[43] -0.12595512 0.87262330 -0.34777501 -2.04723082 -0.34636989 -2.07148363
[49] -2.35551047 -1.81690506 -0.92111044 -0.54687084 -1.37454708 1.04827270
[55] -0.70978934 -0.17212625 0.85218953 -0.95259330 -1.66392563 0.25761261
[61] -0.57133022 0.34770256 -0.17881049 0.16044804 -1.30481497 0.55937758
[67] 0.19757804 -0.65513603 0.57528962 -1.55201811 0.58806527 -0.18124386
[73] 0.11128344 -0.44191918 1.40177110 -0.68171644 2.08511103 0.07637645
[79] -0.58957677 -1.28548694 0.49805599 0.15064732 -1.29405226 -0.69274424
[85] 0.16011624 -0.77280163 0.52660980 1.71723995 -0.29966627 0.22712113
[91] -0.66271943 1.33134109 0.46419295 -0.06668299 1.63273817 0.13662994
[97] -0.07695526 -0.54742458 -1.10144068 -0.45110518
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.8580454 -0.6858238 1.478404 -0.3846254 -1.082643 -0.2538191 -0.03840864
[2,] -0.8580454 -0.6858238 1.478404 -0.3846254 -1.082643 -0.2538191 -0.03840864
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.4320495 -1.950626 -0.3654385 -0.1296234 -0.771934 0.5698443 -1.633132
[2,] 0.4320495 -1.950626 -0.3654385 -0.1296234 -0.771934 0.5698443 -1.633132
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -0.7246077 -1.632752 -1.140659 -1.093091 -1.804833 1.460415 -0.7876658
[2,] -0.7246077 -1.632752 -1.140659 -1.093091 -1.804833 1.460415 -0.7876658
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 0.5402169 0.8222314 0.1847344 -1.905237 0.5887744 -0.387284 -0.4417799
[2,] 0.5402169 0.8222314 0.1847344 -1.905237 0.5887744 -0.387284 -0.4417799
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] -1.673405 0.6893033 0.9611005 -0.1345602 0.5209609 0.2259989 0.1336953
[2,] -1.673405 0.6893033 0.9611005 -0.1345602 0.5209609 0.2259989 0.1336953
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -0.1534175 -1.203182 -0.5513586 -2.142407 0.5356241 -1.34381 0.6886663
[2,] -0.1534175 -1.203182 -0.5513586 -2.142407 0.5356241 -1.34381 0.6886663
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.1259551 0.8726233 -0.347775 -2.047231 -0.3463699 -2.071484 -2.35551
[2,] -0.1259551 0.8726233 -0.347775 -2.047231 -0.3463699 -2.071484 -2.35551
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -1.816905 -0.9211104 -0.5468708 -1.374547 1.048273 -0.7097893 -0.1721262
[2,] -1.816905 -0.9211104 -0.5468708 -1.374547 1.048273 -0.7097893 -0.1721262
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 0.8521895 -0.9525933 -1.663926 0.2576126 -0.5713302 0.3477026 -0.1788105
[2,] 0.8521895 -0.9525933 -1.663926 0.2576126 -0.5713302 0.3477026 -0.1788105
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.160448 -1.304815 0.5593776 0.197578 -0.655136 0.5752896 -1.552018
[2,] 0.160448 -1.304815 0.5593776 0.197578 -0.655136 0.5752896 -1.552018
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] 0.5880653 -0.1812439 0.1112834 -0.4419192 1.401771 -0.6817164 2.085111
[2,] 0.5880653 -0.1812439 0.1112834 -0.4419192 1.401771 -0.6817164 2.085111
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 0.07637645 -0.5895768 -1.285487 0.498056 0.1506473 -1.294052 -0.6927442
[2,] 0.07637645 -0.5895768 -1.285487 0.498056 0.1506473 -1.294052 -0.6927442
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] 0.1601162 -0.7728016 0.5266098 1.71724 -0.2996663 0.2271211 -0.6627194
[2,] 0.1601162 -0.7728016 0.5266098 1.71724 -0.2996663 0.2271211 -0.6627194
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] 1.331341 0.4641929 -0.06668299 1.632738 0.1366299 -0.07695526 -0.5474246
[2,] 1.331341 0.4641929 -0.06668299 1.632738 0.1366299 -0.07695526 -0.5474246
[,99] [,100]
[1,] -1.101441 -0.4511052
[2,] -1.101441 -0.4511052
>
>
> Max(tmp2)
[1] 2.383243
> Min(tmp2)
[1] -2.016748
> mean(tmp2)
[1] 0.05795553
> Sum(tmp2)
[1] 5.795553
> Var(tmp2)
[1] 0.8242068
>
> rowMeans(tmp2)
[1] 0.97942476 0.06673749 0.27384792 0.73362206 -1.46284290 0.99634847
[7] -1.86896668 -0.32223538 0.97328023 -0.91138464 -0.87361286 1.51821446
[13] 0.31072453 0.90165888 -1.38950575 0.38640348 -0.33983148 -2.01674773
[19] 1.18214776 0.32807532 -1.05043825 -1.62599588 -1.54456614 -1.12548882
[25] -1.01798259 -0.08972927 -0.88881408 -0.68953725 0.67913817 -0.60581855
[31] -0.79959436 0.20733157 -0.94556026 0.09951913 1.45726954 1.01894641
[37] 1.39918857 0.44811897 0.17390417 0.25371533 -0.25147748 1.31224593
[43] -1.01226395 1.16275740 1.04427675 0.32887689 -1.41999717 -1.15568490
[49] -0.31460325 0.85292392 2.38324333 0.41277228 -0.12901493 1.59369262
[55] -0.87157162 -0.60709082 0.03617001 -0.66638260 0.54010220 -0.31953269
[61] 0.33848126 -0.32654753 -0.50688617 -0.84216431 0.27227745 -1.59250301
[67] -0.20887867 -0.94705554 0.06336143 0.40637301 -0.20286585 0.52013078
[73] 0.55267514 -1.62333368 0.22881096 1.65303119 0.23064462 0.02732599
[79] 1.33870766 1.22403939 0.90250386 0.48611387 0.24802790 -0.17377316
[85] 0.89010143 -0.54059046 0.93461145 0.19992617 0.33191220 0.07996532
[91] 0.07969607 0.10185860 -0.12225144 1.50317852 0.12917429 0.33411512
[97] 0.85455230 0.40328299 -0.45115513 1.26027237
> rowSums(tmp2)
[1] 0.97942476 0.06673749 0.27384792 0.73362206 -1.46284290 0.99634847
[7] -1.86896668 -0.32223538 0.97328023 -0.91138464 -0.87361286 1.51821446
[13] 0.31072453 0.90165888 -1.38950575 0.38640348 -0.33983148 -2.01674773
[19] 1.18214776 0.32807532 -1.05043825 -1.62599588 -1.54456614 -1.12548882
[25] -1.01798259 -0.08972927 -0.88881408 -0.68953725 0.67913817 -0.60581855
[31] -0.79959436 0.20733157 -0.94556026 0.09951913 1.45726954 1.01894641
[37] 1.39918857 0.44811897 0.17390417 0.25371533 -0.25147748 1.31224593
[43] -1.01226395 1.16275740 1.04427675 0.32887689 -1.41999717 -1.15568490
[49] -0.31460325 0.85292392 2.38324333 0.41277228 -0.12901493 1.59369262
[55] -0.87157162 -0.60709082 0.03617001 -0.66638260 0.54010220 -0.31953269
[61] 0.33848126 -0.32654753 -0.50688617 -0.84216431 0.27227745 -1.59250301
[67] -0.20887867 -0.94705554 0.06336143 0.40637301 -0.20286585 0.52013078
[73] 0.55267514 -1.62333368 0.22881096 1.65303119 0.23064462 0.02732599
[79] 1.33870766 1.22403939 0.90250386 0.48611387 0.24802790 -0.17377316
[85] 0.89010143 -0.54059046 0.93461145 0.19992617 0.33191220 0.07996532
[91] 0.07969607 0.10185860 -0.12225144 1.50317852 0.12917429 0.33411512
[97] 0.85455230 0.40328299 -0.45115513 1.26027237
> 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] 0.97942476 0.06673749 0.27384792 0.73362206 -1.46284290 0.99634847
[7] -1.86896668 -0.32223538 0.97328023 -0.91138464 -0.87361286 1.51821446
[13] 0.31072453 0.90165888 -1.38950575 0.38640348 -0.33983148 -2.01674773
[19] 1.18214776 0.32807532 -1.05043825 -1.62599588 -1.54456614 -1.12548882
[25] -1.01798259 -0.08972927 -0.88881408 -0.68953725 0.67913817 -0.60581855
[31] -0.79959436 0.20733157 -0.94556026 0.09951913 1.45726954 1.01894641
[37] 1.39918857 0.44811897 0.17390417 0.25371533 -0.25147748 1.31224593
[43] -1.01226395 1.16275740 1.04427675 0.32887689 -1.41999717 -1.15568490
[49] -0.31460325 0.85292392 2.38324333 0.41277228 -0.12901493 1.59369262
[55] -0.87157162 -0.60709082 0.03617001 -0.66638260 0.54010220 -0.31953269
[61] 0.33848126 -0.32654753 -0.50688617 -0.84216431 0.27227745 -1.59250301
[67] -0.20887867 -0.94705554 0.06336143 0.40637301 -0.20286585 0.52013078
[73] 0.55267514 -1.62333368 0.22881096 1.65303119 0.23064462 0.02732599
[79] 1.33870766 1.22403939 0.90250386 0.48611387 0.24802790 -0.17377316
[85] 0.89010143 -0.54059046 0.93461145 0.19992617 0.33191220 0.07996532
[91] 0.07969607 0.10185860 -0.12225144 1.50317852 0.12917429 0.33411512
[97] 0.85455230 0.40328299 -0.45115513 1.26027237
> rowMin(tmp2)
[1] 0.97942476 0.06673749 0.27384792 0.73362206 -1.46284290 0.99634847
[7] -1.86896668 -0.32223538 0.97328023 -0.91138464 -0.87361286 1.51821446
[13] 0.31072453 0.90165888 -1.38950575 0.38640348 -0.33983148 -2.01674773
[19] 1.18214776 0.32807532 -1.05043825 -1.62599588 -1.54456614 -1.12548882
[25] -1.01798259 -0.08972927 -0.88881408 -0.68953725 0.67913817 -0.60581855
[31] -0.79959436 0.20733157 -0.94556026 0.09951913 1.45726954 1.01894641
[37] 1.39918857 0.44811897 0.17390417 0.25371533 -0.25147748 1.31224593
[43] -1.01226395 1.16275740 1.04427675 0.32887689 -1.41999717 -1.15568490
[49] -0.31460325 0.85292392 2.38324333 0.41277228 -0.12901493 1.59369262
[55] -0.87157162 -0.60709082 0.03617001 -0.66638260 0.54010220 -0.31953269
[61] 0.33848126 -0.32654753 -0.50688617 -0.84216431 0.27227745 -1.59250301
[67] -0.20887867 -0.94705554 0.06336143 0.40637301 -0.20286585 0.52013078
[73] 0.55267514 -1.62333368 0.22881096 1.65303119 0.23064462 0.02732599
[79] 1.33870766 1.22403939 0.90250386 0.48611387 0.24802790 -0.17377316
[85] 0.89010143 -0.54059046 0.93461145 0.19992617 0.33191220 0.07996532
[91] 0.07969607 0.10185860 -0.12225144 1.50317852 0.12917429 0.33411512
[97] 0.85455230 0.40328299 -0.45115513 1.26027237
>
> colMeans(tmp2)
[1] 0.05795553
> colSums(tmp2)
[1] 5.795553
> colVars(tmp2)
[1] 0.8242068
> colSd(tmp2)
[1] 0.9078584
> colMax(tmp2)
[1] 2.383243
> colMin(tmp2)
[1] -2.016748
> colMedians(tmp2)
[1] 0.1515392
> colRanges(tmp2)
[,1]
[1,] -2.016748
[2,] 2.383243
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] 1.4730092 -3.7148364 -3.0887814 0.5600148 -0.9989025 5.3547098
[7] 0.7996411 4.2710467 -3.2441429 1.7771556
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.4115023
[2,] -0.1496301
[3,] 0.2801175
[4,] 0.5996459
[5,] 1.1220233
>
> rowApply(tmp,sum)
[1] 2.682133 -2.022021 5.299810 -2.110478 2.947063 -2.008808 -6.846106
[8] 2.425857 6.033046 -3.211581
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 6 10 5 7 6 4 3 8 4 5
[2,] 3 3 1 3 2 8 6 4 7 8
[3,] 1 6 6 2 9 2 5 3 3 7
[4,] 10 5 4 5 3 5 9 9 6 1
[5,] 7 7 3 1 5 3 2 7 10 3
[6,] 9 2 7 9 10 6 4 10 8 10
[7,] 4 8 9 8 1 7 8 6 2 6
[8,] 5 9 10 10 4 9 7 2 1 9
[9,] 2 1 2 6 8 10 1 1 9 2
[10,] 8 4 8 4 7 1 10 5 5 4
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 4.73941465 -2.57251076 2.15455077 -1.67367469 0.30601712 0.98654547
[7] -1.82354559 0.87260572 -0.02168038 1.28602238 1.51866059 -0.25128096
[13] -0.13549292 -2.28901041 -4.16793703 -1.62868049 -2.50559601 4.30297747
[19] -0.70223238 0.33298211
> colApply(tmp,quantile)[,1]
[,1]
[1,] 0.07920005
[2,] 0.57818478
[3,] 1.08103346
[4,] 1.08147961
[5,] 1.91951675
>
> rowApply(tmp,sum)
[1] -3.294638 -3.250268 2.001409 -2.246180 5.517812
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 12 19 19 17 14
[2,] 3 3 2 7 11
[3,] 15 4 20 5 16
[4,] 1 13 5 18 6
[5,] 16 9 11 3 17
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.07920005 -0.8205020 0.4381639 -1.8256511 0.47587104 0.8228231
[2,] 1.08103346 -1.0160418 -0.8526401 0.4164742 -0.21384382 0.8491835
[3,] 1.91951675 -0.7983800 2.1408319 -0.3575537 -0.04571979 0.1133088
[4,] 0.57818478 -0.5846766 -0.7902316 0.8724427 -1.21089804 0.1676683
[5,] 1.08147961 0.6470896 1.2184266 -0.7793869 1.30060773 -0.9664381
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.7350831 -0.08090124 0.42934928 -0.02735309 0.6037154 -0.6281581
[2,] 0.3839427 0.50079775 0.81312639 -0.66484571 -0.6672654 -0.8071639
[3,] -0.6391451 0.08018152 -0.19899582 -0.53269957 -0.2388675 -0.2152149
[4,] 0.1747557 -0.37470976 0.08696149 0.50119519 1.5058184 0.3075800
[5,] -1.0080157 0.74723746 -1.15212171 2.00972556 0.3152597 1.0916760
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -1.62378532 -0.53791040 -0.4378288 0.7933309 0.1771870 -0.49105003
[2,] -0.01675524 -0.17361995 -2.1691223 -2.1126286 0.4816979 1.16284087
[3,] 0.38148316 0.07585087 -0.1868046 0.1449191 -0.2404779 0.08025589
[4,] 0.11072897 -1.45860989 -0.7137132 0.4217796 -1.1192203 1.39432333
[5,] 1.01283550 -0.19472103 -0.6604681 -0.8760814 -1.8047827 2.15660740
[,19] [,20]
[1,] -0.6392188 0.7331630
[2,] -0.7833630 0.5379247
[3,] 1.4940416 -0.9751215
[4,] -0.3871798 -1.7283792
[5,] -0.3865123 1.7653951
>
>
> 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 : 648 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 562 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-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 -0.5284426 -0.399639 -1.040632 0.5831749 0.07664058 0.9177905 -0.2350749
col8 col9 col10 col11 col12 col13 col14
row1 0.3236032 0.8122733 -1.537257 -0.3727371 1.493008 -0.5902706 -0.8803162
col15 col16 col17 col18 col19 col20
row1 0.265805 -0.8651347 -0.5480399 1.55172 0.6599217 0.0564668
> tmp[,"col10"]
col10
row1 -1.5372573
row2 -1.0632152
row3 -1.3180476
row4 0.2392897
row5 -0.5126502
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6
row1 -0.52844260 -0.399639 -1.040632 0.58317494 0.07664058 0.9177905
row5 -0.09334992 1.481098 -1.565592 -0.04533762 3.08818556 -0.7764631
col7 col8 col9 col10 col11 col12
row1 -0.23507490 0.3236032 0.8122733 -1.5372573 -0.3727371 1.4930078
row5 -0.09486808 -0.6770810 1.0321814 -0.5126502 -1.0238734 0.2190476
col13 col14 col15 col16 col17 col18 col19
row1 -0.5902706 -0.8803162 0.2658050 -0.8651347 -0.5480399 1.5517198 0.6599217
row5 -0.3549636 0.1622418 0.9556698 -0.5208569 1.5419920 0.2322511 -0.5728321
col20
row1 0.0564668
row5 -1.7575023
> tmp[,c("col6","col20")]
col6 col20
row1 0.9177905 0.05646680
row2 -1.8198931 0.19816976
row3 1.6326763 -0.03152154
row4 1.3327580 -0.17246802
row5 -0.7764631 -1.75750227
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.9177905 0.0564668
row5 -0.7764631 -1.7575023
>
>
>
>
> 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 51.04537 49.45764 51.45948 50.66747 51.11388 105.3323 50.1159 48.59531
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.04729 48.81837 51.26516 49.14453 50.0793 50.32813 50.10559 50.47178
col17 col18 col19 col20
row1 49.28784 51.2867 50.04421 105.8903
> tmp[,"col10"]
col10
row1 48.81837
row2 31.31852
row3 28.29000
row4 31.29443
row5 52.07455
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 51.04537 49.45764 51.45948 50.66747 51.11388 105.3323 50.11590 48.59531
row5 49.04569 50.20072 50.95699 53.02277 50.78641 106.9406 49.66156 51.26551
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.04729 48.81837 51.26516 49.14453 50.07930 50.32813 50.10559 50.47178
row5 49.27480 52.07455 50.54387 51.21973 49.04935 50.77444 50.29335 50.25985
col17 col18 col19 col20
row1 49.28784 51.28670 50.04421 105.8903
row5 49.69971 48.44373 49.65174 105.7714
> tmp[,c("col6","col20")]
col6 col20
row1 105.33228 105.89027
row2 74.85309 73.39461
row3 75.44545 74.06255
row4 73.67334 74.57114
row5 106.94059 105.77141
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 105.3323 105.8903
row5 106.9406 105.7714
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 105.3323 105.8903
row5 106.9406 105.7714
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 1.4127296
[2,] 0.6391291
[3,] 1.1163746
[4,] 1.2296902
[5,] -1.6282707
> tmp[,c("col17","col7")]
col17 col7
[1,] -1.6119551 -1.0852852
[2,] -0.1008693 0.3582627
[3,] -1.0051549 -0.2113117
[4,] 0.1887043 0.8616609
[5,] -1.7008302 1.0064665
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 0.3461760 1.3480064
[2,] -0.7008144 0.5506389
[3,] -0.2676918 -0.2992285
[4,] 0.1987774 -0.2383568
[5,] 1.7294838 2.0923967
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 0.346176
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 0.3461760
[2,] -0.7008144
>
>
>
> 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 0.8023841 -1.02930253 -0.4808674 -0.7019512 -0.04372833 0.1893008
row1 -0.9498729 0.06279884 0.8915976 0.4544946 0.34824497 -1.2127253
[,7] [,8] [,9] [,10] [,11] [,12] [,13]
row3 -0.28761877 0.0244520 -1.355817 0.2088572 0.4605301 0.4551726 -1.315987
row1 0.07988905 0.2065743 1.386576 -0.4063833 -0.4070933 0.0507891 -0.278340
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row3 0.1298614 -0.4271317 0.8923769 0.2693856 0.7962524 -0.56660032 -1.4350622
row1 0.7325515 -0.3132844 0.4949333 2.2303692 -0.6214307 -0.09307695 0.1555473
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -0.3443332 -1.313713 -1.474741 0.9934403 -0.7761203 -1.116498 0.6428028
[,8] [,9] [,10]
row2 -0.386776 -0.3969832 -0.6453466
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -0.5915755 0.03864724 -0.7033599 -1.635788 -0.4153095 0.2017046 0.8738295
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.3957128 0.1514113 -1.161166 1.228734 -1.413419 1.104333 1.468252
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.3183905 -1.073902 -0.1367872 -1.113111 1.846917 0.8949282
>
>
> 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: 0x6155db3317a0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3c04431ad683"
[2] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3c044551e9707"
[3] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3c0447b2c4424"
[4] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3c044450ec181"
[5] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3c04462023da9"
[6] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3c0443f86e769"
[7] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3c0443df6b83"
[8] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3c04440bd0ebb"
[9] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3c0442cbc7971"
[10] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3c0441b9517fd"
[11] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3c044578fd732"
[12] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3c0445815a07"
[13] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3c0441699a090"
[14] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3c04432e9b855"
[15] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3c0441d0782ea"
>
>
> ### 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: 0x6155da0bbd40>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x6155da0bbd40>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x6155da0bbd40>
> rowMedians(tmp)
[1] 0.043375888 -0.205764996 0.290071725 -0.257086084 0.078946202
[6] 0.116604825 -0.222887306 -0.231109291 0.036329803 -0.054633083
[11] 0.326960779 0.053421254 -0.117579910 0.434207600 -0.994177925
[16] 0.082031338 0.370117940 -0.563357785 0.200413609 -0.044728266
[21] 0.122792666 -0.015596885 -0.119823624 -0.005415343 0.527318630
[26] -0.113213749 -0.192779982 -0.177669926 0.480730134 0.435370753
[31] 0.140402926 -0.278410730 -0.662955769 -0.384005141 -0.657734662
[36] -0.197392618 0.066961393 0.051347995 0.073509906 -0.002484840
[41] 0.115571722 -0.084398455 -0.268112027 -0.392512250 -0.372186744
[46] 0.347918859 0.619032797 -0.026046258 0.033376212 -0.118982094
[51] -0.028364836 -0.286825983 0.556879026 -0.031235435 0.076124452
[56] -0.073831428 0.453538699 0.195714502 -0.121792092 0.033942901
[61] -0.394379510 -0.089971057 0.489647442 0.276960626 0.121557063
[66] 0.141666512 0.133152596 0.119345371 -0.074662285 0.125941858
[71] -0.219432366 -0.124980522 0.595562236 -0.192456072 -0.108869830
[76] 0.287895254 -0.376310327 -0.409071193 -0.042974326 0.038090469
[81] -0.463091143 0.384585140 0.194444189 0.313886702 0.168710034
[86] 0.116954968 0.106847328 0.089662010 -0.012381226 0.257794932
[91] 0.020722044 -0.647141560 -0.547168421 -0.379137601 -0.412740906
[96] 0.344359582 0.023452805 -0.133665351 0.420108720 0.227661969
[101] 0.079671788 0.172013556 0.137245797 0.001118841 0.019535949
[106] 0.025192908 -0.224884110 -0.180020279 0.205593387 -0.049148838
[111] 0.217034886 0.570825277 -0.038824588 0.350309547 0.164834724
[116] 0.746322497 0.617061038 0.031497752 0.273325923 0.022450778
[121] -0.092064484 0.427515345 0.191641492 -0.858081809 -0.426997129
[126] -0.033319410 0.004970518 0.488554936 -0.323531758 -0.806096710
[131] 0.169238744 -0.244793308 0.337208866 -0.124963279 0.203026149
[136] -0.081436559 0.148123986 -0.880206752 -0.173129887 -0.117107197
[141] 0.355836009 0.011741475 0.007719007 0.158336354 -0.131352446
[146] -0.281405323 0.200454805 -0.277413340 0.030216591 0.108487372
[151] 0.113984622 0.573717847 0.204497283 -0.030869729 -0.867402141
[156] 0.359307855 0.122469147 -0.103114901 -0.076673020 0.526901891
[161] -0.147817906 0.054377101 0.423044133 -0.009203509 -0.110171775
[166] 0.097618754 0.245712329 0.249196574 0.258557029 -0.299425560
[171] 0.112320406 0.074423926 0.327099950 0.312340564 -0.291086230
[176] 0.176382273 -0.044755445 -0.042591093 -0.540201148 0.113105900
[181] 0.756603475 -0.218123336 0.097750777 0.174975436 0.012021905
[186] 0.558574763 0.231001642 0.247270084 -0.049422841 -0.120724264
[191] 0.013777056 0.388791604 0.334929367 0.381294008 -0.047746354
[196] -0.256186789 0.316193947 0.166653613 0.167642509 -0.345081803
[201] 0.303503373 0.301631787 0.289033917 -0.448727668 0.237203564
[206] 0.053011144 0.509068524 -0.111797597 0.343541481 0.236238340
[211] 0.004270467 0.254787458 0.419190748 0.196680743 0.229255533
[216] 0.138308698 0.396298902 0.121763667 0.013276390 0.083899369
[221] 0.037959193 0.288539928 -0.390754456 -0.121200311 -0.083368005
[226] 0.104242600 -0.345635148 -0.081182652 0.196791327 0.260343582
>
> proc.time()
user system elapsed
1.351 1.480 2.815
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
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: 0x5e02aef22ff0>
> .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: 0x5e02aef22ff0>
> .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: 0x5e02aef22ff0>
> .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: 0x5e02aef22ff0>
> 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: 0x5e02aebce710>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e02aebce710>
> .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: 0x5e02aebce710>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e02aebce710>
> .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: 0x5e02aebce710>
> 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: 0x5e02aee157d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e02aee157d0>
> .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: 0x5e02aee157d0>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5e02aee157d0>
> .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: 0x5e02aee157d0>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x5e02aee157d0>
> .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: 0x5e02aee157d0>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x5e02aee157d0>
> .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: 0x5e02aee157d0>
> 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: 0x5e02af058830>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x5e02af058830>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e02af058830>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e02af058830>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile3c07233eb90e4" "BufferedMatrixFile3c0727e2f6b62"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile3c07233eb90e4" "BufferedMatrixFile3c0727e2f6b62"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e02b0251e10>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e02b0251e10>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5e02b0251e10>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5e02b0251e10>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x5e02b0251e10>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x5e02b0251e10>
> .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: 0x5e02b023cc20>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e02b023cc20>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5e02b023cc20>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x5e02b023cc20>
> 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: 0x5e02af4d2e10>
> .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: 0x5e02af4d2e10>
> rm(P)
>
> proc.time()
user system elapsed
0.251 0.051 0.292
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
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
>
> Temp <- createBufferedMatrix(100)
> dim(Temp)
[1] 100 0
> buffer.dim(Temp)
[1] 1 1
>
>
> proc.time()
user system elapsed
0.234 0.047 0.270