Ben Bolstad
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/BufferedMatrix |
| Branch: RELEASE_3_11 |
| Last Commit: c4ad43d |
| Last Changed Date: 2020-04-27 14:14:34 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:58:09 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE BufferedMatrix PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 210/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BufferedMatrix 1.52.0 Ben Bolstad
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK | |
| Package: BufferedMatrix |
| Version: 1.52.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BufferedMatrix_1.52.0.tar.gz |
| StartedAt: 2020-10-16 23:16:41 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 23:17:32 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 51.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BufferedMatrix_1.52.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK * this is package ‘BufferedMatrix’ version ‘1.52.0’ * 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 * 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE prepare_Rd: createBufferedMatrix.Rd:26: Dropping empty section \keyword prepare_Rd: createBufferedMatrix.Rd:17-18: Dropping empty section \details prepare_Rd: createBufferedMatrix.Rd:15-16: Dropping empty section \value prepare_Rd: createBufferedMatrix.Rd:19-20: Dropping empty section \references prepare_Rd: createBufferedMatrix.Rd:21-22: Dropping empty section \seealso prepare_Rd: createBufferedMatrix.Rd:23-24: Dropping empty section \examples * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... NONE * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘Rcodetesting.R’ Running ‘c_code_level_tests.R’ Running ‘objectTesting.R’ Running ‘rawCalltesting.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/00check.log’ for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘BufferedMatrix’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c RBufferedMatrix.c -o RBufferedMatrix.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c:1580:7: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
if (!(Matrix->readonly) & setting){
^ ~
doubleBufferedMatrix.c:1580:7: note: add parentheses after the '!' to evaluate the bitwise operator first
if (!(Matrix->readonly) & setting){
^
( )
doubleBufferedMatrix.c:1580:7: note: add parentheses around left hand side expression to silence this warning
if (!(Matrix->readonly) & setting){
^
( )
doubleBufferedMatrix.c:3327:12: warning: unused function 'sort_double' [-Wunused-function]
static int sort_double(const double *a1,const double *a2){
^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c init_package.c -o init_package.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘rowMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘rowSums’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colSums’ in package ‘BufferedMatrix’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘BufferedMatrix’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘BufferedMatrix’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BufferedMatrix)
BufferedMatrix.Rcheck/tests/c_code_level_tests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
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
0.544 0.134 0.656
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
>
> ### this is used to control how many repetitions in something below
> ### higher values result in more checks.
> nreps <-100 ##20000
>
>
> ## test creation and some simple assignments and subsetting operations
>
> ## first on single elements
> tmp <- createBufferedMatrix(1000,10)
>
> tmp[10,5]
[1] 0
> tmp[10,5] <- 10
> tmp[10,5]
[1] 10
> tmp[10,5] <- 12.445
> tmp[10,5]
[1] 12.445
>
>
>
> ## now testing accessing multiple elements
> tmp2 <- createBufferedMatrix(10,20)
>
>
> tmp2[3,1] <- 51.34
> tmp2[9,2] <- 9.87654
> tmp2[,1:2]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[,-(3:20)]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 51.34 0 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
> tmp2[-3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0
[5,] 0 0 0 0 0 0 0
[6,] 0 0 0 0 0 0 0
[7,] 0 0 0 0 0 0 0
[8,] 0 0 0 0 0 0 0
[9,] 0 0 0 0 0 0 0
> tmp2[2,1:3]
[,1] [,2] [,3]
[1,] 0 0 0
> tmp2[3:9,1:3]
[,1] [,2] [,3]
[1,] 51.34 0.00000 0
[2,] 0.00 0.00000 0
[3,] 0.00 0.00000 0
[4,] 0.00 0.00000 0
[5,] 0.00 0.00000 0
[6,] 0.00 0.00000 0
[7,] 0.00 9.87654 0
> tmp2[-4,-4]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 51.34 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0.00 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19]
[1,] 0 0 0 0 0 0
[2,] 0 0 0 0 0 0
[3,] 0 0 0 0 0 0
[4,] 0 0 0 0 0 0
[5,] 0 0 0 0 0 0
[6,] 0 0 0 0 0 0
[7,] 0 0 0 0 0 0
[8,] 0 0 0 0 0 0
[9,] 0 0 0 0 0 0
>
> ## now testing accessing/assigning multiple elements
> tmp3 <- createBufferedMatrix(10,10)
>
> for (i in 1:10){
+ for (j in 1:10){
+ tmp3[i,j] <- (j-1)*10 + i
+ }
+ }
>
> tmp3[2:4,2:4]
[,1] [,2] [,3]
[1,] 12 22 32
[2,] 13 23 33
[3,] 14 24 34
> tmp3[c(-10),c(2:4,2:4,10,1,2,1:10,10:1)]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 11 21 31 11 21 31 91 1 11 1 11 21 31
[2,] 12 22 32 12 22 32 92 2 12 2 12 22 32
[3,] 13 23 33 13 23 33 93 3 13 3 13 23 33
[4,] 14 24 34 14 24 34 94 4 14 4 14 24 34
[5,] 15 25 35 15 25 35 95 5 15 5 15 25 35
[6,] 16 26 36 16 26 36 96 6 16 6 16 26 36
[7,] 17 27 37 17 27 37 97 7 17 7 17 27 37
[8,] 18 28 38 18 28 38 98 8 18 8 18 28 38
[9,] 19 29 39 19 29 39 99 9 19 9 19 29 39
[,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
[1,] 41 51 61 71 81 91 91 81 71 61 51 41
[2,] 42 52 62 72 82 92 92 82 72 62 52 42
[3,] 43 53 63 73 83 93 93 83 73 63 53 43
[4,] 44 54 64 74 84 94 94 84 74 64 54 44
[5,] 45 55 65 75 85 95 95 85 75 65 55 45
[6,] 46 56 66 76 86 96 96 86 76 66 56 46
[7,] 47 57 67 77 87 97 97 87 77 67 57 47
[8,] 48 58 68 78 88 98 98 88 78 68 58 48
[9,] 49 59 69 79 89 99 99 89 79 69 59 49
[,26] [,27] [,28] [,29]
[1,] 31 21 11 1
[2,] 32 22 12 2
[3,] 33 23 13 3
[4,] 34 24 14 4
[5,] 35 25 15 5
[6,] 36 26 16 6
[7,] 37 27 17 7
[8,] 38 28 18 8
[9,] 39 29 19 9
> tmp3[-c(1:5),-c(6:10)]
[,1] [,2] [,3] [,4] [,5]
[1,] 6 16 26 36 46
[2,] 7 17 27 37 47
[3,] 8 18 28 38 48
[4,] 9 19 29 39 49
[5,] 10 20 30 40 50
>
> ## assignment of whole columns
> tmp3[,1] <- c(1:10*100.0)
> tmp3[,1:2] <- tmp3[,1:2]*100
> tmp3[,1:2] <- tmp3[,2:1]
> tmp3[,1:2]
[,1] [,2]
[1,] 1100 1e+04
[2,] 1200 2e+04
[3,] 1300 3e+04
[4,] 1400 4e+04
[5,] 1500 5e+04
[6,] 1600 6e+04
[7,] 1700 7e+04
[8,] 1800 8e+04
[9,] 1900 9e+04
[10,] 2000 1e+05
>
>
> tmp3[,-1] <- tmp3[,1:9]
> tmp3[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1100 1100 1e+04 21 31 41 51 61 71 81
[2,] 1200 1200 2e+04 22 32 42 52 62 72 82
[3,] 1300 1300 3e+04 23 33 43 53 63 73 83
[4,] 1400 1400 4e+04 24 34 44 54 64 74 84
[5,] 1500 1500 5e+04 25 35 45 55 65 75 85
[6,] 1600 1600 6e+04 26 36 46 56 66 76 86
[7,] 1700 1700 7e+04 27 37 47 57 67 77 87
[8,] 1800 1800 8e+04 28 38 48 58 68 78 88
[9,] 1900 1900 9e+04 29 39 49 59 69 79 89
[10,] 2000 2000 1e+05 30 40 50 60 70 80 90
>
> tmp3[,1:2] <- rep(1,10)
> tmp3[,1:2] <- rep(1,20)
> tmp3[,1:2] <- matrix(c(1:5),1,5)
>
> tmp3[,-c(1:8)] <- matrix(c(1:5),1,5)
>
> tmp3[1,] <- 1:10
> tmp3[1,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
> tmp3[-1,] <- c(1,2)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 2 1 2 1 2 1 2 1 2 1
[10,] 1 2 1 2 1 2 1 2 1 2
> tmp3[-c(1:8),] <- matrix(c(1:5),1,5)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 1 3 5 2 4 1 3 5 2 4
[10,] 2 4 1 3 5 2 4 1 3 5
>
>
> tmp3[1:2,1:2] <- 5555.04
> tmp3[-(1:2),1:2] <- 1234.56789
>
>
>
> ## testing accessors for the directory and prefix
> directory(tmp3)
[1] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests"
> prefix(tmp3)
[1] "BM"
>
> ## testing if we can remove these objects
> rm(tmp, tmp2, tmp3)
> gc()
used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
Ncells 442464 23.7 955235 51.1 NA 617894 33.0
Vcells 798850 6.1 8388608 64.0 65536 1932312 14.8
>
>
>
>
> ##
> ## 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 Oct 16 23:17:07 2020"
> 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 Oct 16 23:17:07 2020"
>
>
> 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: 0x7fd7e5691540>
>
>
>
> 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 Oct 16 23:17:10 2020"
> 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 Oct 16 23:17:12 2020"
>
> ColMode(tmp2)
<pointer: 0x7fd7e5691540>
>
>
>
> ### 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,] 99.361547041 0.05938395 -0.2969439 -0.2703964
[2,] 0.003165862 0.83713917 0.5799696 1.9087366
[3,] 0.510973392 -0.75992794 0.5834485 -0.9852039
[4,] 0.267952116 1.74475431 0.5803223 -0.8245759
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.11-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,] 99.361547041 0.05938395 0.2969439 0.2703964
[2,] 0.003165862 0.83713917 0.5799696 1.9087366
[3,] 0.510973392 0.75992794 0.5834485 0.9852039
[4,] 0.267952116 1.74475431 0.5803223 0.8245759
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.11-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,] 9.96802624 0.2436882 0.5449256 0.5199965
[2,] 0.05626599 0.9149531 0.7615573 1.3815703
[3,] 0.71482403 0.8717385 0.7638380 0.9925744
[4,] 0.51764091 1.3208915 0.7617889 0.9080616
>
> my.function <- function(x,power){
+ (x+5)^power
+ }
>
> ewApply(tmp5,my.function,power=2)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.11-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,] 224.04181 27.49627 30.74620 30.47036
[2,] 25.56583 34.98667 33.19554 40.72444
[3,] 32.65921 34.47731 33.22183 35.91095
[4,] 30.44436 39.95367 33.19821 34.90519
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x7fd80540efe0>
> exp(tmp5)
<pointer: 0x7fd80540efe0>
> log(tmp5,2)
<pointer: 0x7fd80540efe0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 466.3137
> Min(tmp5)
[1] 53.21192
> mean(tmp5)
[1] 72.65547
> Sum(tmp5)
[1] 14531.09
> Var(tmp5)
[1] 870.2119
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 86.60820 71.78914 72.02966 73.58550 67.67421 71.43616 72.44330 70.57849
[9] 69.34805 71.06202
> rowSums(tmp5)
[1] 1732.164 1435.783 1440.593 1471.710 1353.484 1428.723 1448.866 1411.570
[9] 1386.961 1421.240
> rowVars(tmp5)
[1] 8063.84540 70.13152 44.09427 93.36080 63.26250 117.74847
[7] 149.17445 92.10295 62.59741 104.50958
> rowSd(tmp5)
[1] 89.798916 8.374457 6.640352 9.662339 7.953773 10.851197 12.213699
[8] 9.597028 7.911853 10.222993
> rowMax(tmp5)
[1] 466.31367 87.32080 81.46000 95.56617 85.08276 91.98516 93.90634
[8] 89.53594 83.28249 91.66329
> rowMin(tmp5)
[1] 56.16307 53.21192 58.72573 59.21205 56.76712 56.17240 54.19644 54.41264
[9] 55.36808 55.68758
>
> colMeans(tmp5)
[1] 106.89763 69.96467 71.43949 70.52543 70.09221 74.81283 67.01753
[8] 68.80122 73.48092 71.17047 69.75730 71.64748 67.05580 66.76839
[15] 73.65418 73.29966 72.20038 71.81403 72.02714 70.68269
> colSums(tmp5)
[1] 1068.9763 699.6467 714.3949 705.2543 700.9221 748.1283 670.1753
[8] 688.0122 734.8092 711.7047 697.5730 716.4748 670.5580 667.6839
[15] 736.5418 732.9966 722.0038 718.1403 720.2714 706.8269
> colVars(tmp5)
[1] 16024.72497 52.43743 53.73081 107.72593 67.43434 127.02597
[7] 84.88255 141.40734 97.58504 104.39935 66.91338 95.58349
[13] 44.29945 70.87631 119.56429 113.74379 34.45127 135.58365
[19] 127.81533 94.97006
> colSd(tmp5)
[1] 126.588803 7.241369 7.330130 10.379110 8.211841 11.270580
[7] 9.213173 11.891482 9.878514 10.217600 8.180060 9.776681
[13] 6.655783 8.418807 10.934546 10.665074 5.869521 11.644039
[19] 11.305544 9.745259
> colMax(tmp5)
[1] 466.31367 83.15833 79.49018 90.66291 82.69284 91.66329 85.53502
[8] 95.56617 89.45584 89.53594 83.20591 91.31119 77.96135 80.04744
[15] 93.90634 91.56892 80.14503 89.51778 91.98516 83.28249
> colMin(tmp5)
[1] 53.21192 57.22988 56.43605 59.93903 58.72573 59.61165 55.36808 55.68758
[9] 56.88135 54.19644 57.79257 60.55080 58.97236 54.57398 59.68411 58.16331
[17] 62.73119 54.41264 56.16307 57.18248
>
>
> ### 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] 86.60820 71.78914 72.02966 73.58550 67.67421 71.43616 NA 70.57849
[9] 69.34805 71.06202
> rowSums(tmp5)
[1] 1732.164 1435.783 1440.593 1471.710 1353.484 1428.723 NA 1411.570
[9] 1386.961 1421.240
> rowVars(tmp5)
[1] 8063.84540 70.13152 44.09427 93.36080 63.26250 117.74847
[7] 156.10489 92.10295 62.59741 104.50958
> rowSd(tmp5)
[1] 89.798916 8.374457 6.640352 9.662339 7.953773 10.851197 12.494194
[8] 9.597028 7.911853 10.222993
> rowMax(tmp5)
[1] 466.31367 87.32080 81.46000 95.56617 85.08276 91.98516 NA
[8] 89.53594 83.28249 91.66329
> rowMin(tmp5)
[1] 56.16307 53.21192 58.72573 59.21205 56.76712 56.17240 NA 54.41264
[9] 55.36808 55.68758
>
> colMeans(tmp5)
[1] 106.89763 69.96467 71.43949 70.52543 70.09221 74.81283 67.01753
[8] 68.80122 73.48092 71.17047 69.75730 71.64748 NA 66.76839
[15] 73.65418 73.29966 72.20038 71.81403 72.02714 70.68269
> colSums(tmp5)
[1] 1068.9763 699.6467 714.3949 705.2543 700.9221 748.1283 670.1753
[8] 688.0122 734.8092 711.7047 697.5730 716.4748 NA 667.6839
[15] 736.5418 732.9966 722.0038 718.1403 720.2714 706.8269
> colVars(tmp5)
[1] 16024.72497 52.43743 53.73081 107.72593 67.43434 127.02597
[7] 84.88255 141.40734 97.58504 104.39935 66.91338 95.58349
[13] NA 70.87631 119.56429 113.74379 34.45127 135.58365
[19] 127.81533 94.97006
> colSd(tmp5)
[1] 126.588803 7.241369 7.330130 10.379110 8.211841 11.270580
[7] 9.213173 11.891482 9.878514 10.217600 8.180060 9.776681
[13] NA 8.418807 10.934546 10.665074 5.869521 11.644039
[19] 11.305544 9.745259
> colMax(tmp5)
[1] 466.31367 83.15833 79.49018 90.66291 82.69284 91.66329 85.53502
[8] 95.56617 89.45584 89.53594 83.20591 91.31119 NA 80.04744
[15] 93.90634 91.56892 80.14503 89.51778 91.98516 83.28249
> colMin(tmp5)
[1] 53.21192 57.22988 56.43605 59.93903 58.72573 59.61165 55.36808 55.68758
[9] 56.88135 54.19644 57.79257 60.55080 NA 54.57398 59.68411 58.16331
[17] 62.73119 54.41264 56.16307 57.18248
>
> Max(tmp5,na.rm=TRUE)
[1] 466.3137
> Min(tmp5,na.rm=TRUE)
[1] 53.21192
> mean(tmp5,na.rm=TRUE)
[1] 72.68075
> Sum(tmp5,na.rm=TRUE)
[1] 14463.47
> Var(tmp5,na.rm=TRUE)
[1] 874.4785
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 86.60820 71.78914 72.02966 73.58550 67.67421 71.43616 72.69684 70.57849
[9] 69.34805 71.06202
> rowSums(tmp5,na.rm=TRUE)
[1] 1732.164 1435.783 1440.593 1471.710 1353.484 1428.723 1381.240 1411.570
[9] 1386.961 1421.240
> rowVars(tmp5,na.rm=TRUE)
[1] 8063.84540 70.13152 44.09427 93.36080 63.26250 117.74847
[7] 156.10489 92.10295 62.59741 104.50958
> rowSd(tmp5,na.rm=TRUE)
[1] 89.798916 8.374457 6.640352 9.662339 7.953773 10.851197 12.494194
[8] 9.597028 7.911853 10.222993
> rowMax(tmp5,na.rm=TRUE)
[1] 466.31367 87.32080 81.46000 95.56617 85.08276 91.98516 93.90634
[8] 89.53594 83.28249 91.66329
> rowMin(tmp5,na.rm=TRUE)
[1] 56.16307 53.21192 58.72573 59.21205 56.76712 56.17240 54.19644 54.41264
[9] 55.36808 55.68758
>
> colMeans(tmp5,na.rm=TRUE)
[1] 106.89763 69.96467 71.43949 70.52543 70.09221 74.81283 67.01753
[8] 68.80122 73.48092 71.17047 69.75730 71.64748 66.99243 66.76839
[15] 73.65418 73.29966 72.20038 71.81403 72.02714 70.68269
> colSums(tmp5,na.rm=TRUE)
[1] 1068.9763 699.6467 714.3949 705.2543 700.9221 748.1283 670.1753
[8] 688.0122 734.8092 711.7047 697.5730 716.4748 602.9319 667.6839
[15] 736.5418 732.9966 722.0038 718.1403 720.2714 706.8269
> colVars(tmp5,na.rm=TRUE)
[1] 16024.72497 52.43743 53.73081 107.72593 67.43434 127.02597
[7] 84.88255 141.40734 97.58504 104.39935 66.91338 95.58349
[13] 49.79171 70.87631 119.56429 113.74379 34.45127 135.58365
[19] 127.81533 94.97006
> colSd(tmp5,na.rm=TRUE)
[1] 126.588803 7.241369 7.330130 10.379110 8.211841 11.270580
[7] 9.213173 11.891482 9.878514 10.217600 8.180060 9.776681
[13] 7.056324 8.418807 10.934546 10.665074 5.869521 11.644039
[19] 11.305544 9.745259
> colMax(tmp5,na.rm=TRUE)
[1] 466.31367 83.15833 79.49018 90.66291 82.69284 91.66329 85.53502
[8] 95.56617 89.45584 89.53594 83.20591 91.31119 77.96135 80.04744
[15] 93.90634 91.56892 80.14503 89.51778 91.98516 83.28249
> colMin(tmp5,na.rm=TRUE)
[1] 53.21192 57.22988 56.43605 59.93903 58.72573 59.61165 55.36808 55.68758
[9] 56.88135 54.19644 57.79257 60.55080 58.97236 54.57398 59.68411 58.16331
[17] 62.73119 54.41264 56.16307 57.18248
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 86.60820 71.78914 72.02966 73.58550 67.67421 71.43616 NaN 70.57849
[9] 69.34805 71.06202
> rowSums(tmp5,na.rm=TRUE)
[1] 1732.164 1435.783 1440.593 1471.710 1353.484 1428.723 0.000 1411.570
[9] 1386.961 1421.240
> rowVars(tmp5,na.rm=TRUE)
[1] 8063.84540 70.13152 44.09427 93.36080 63.26250 117.74847
[7] NA 92.10295 62.59741 104.50958
> rowSd(tmp5,na.rm=TRUE)
[1] 89.798916 8.374457 6.640352 9.662339 7.953773 10.851197 NA
[8] 9.597028 7.911853 10.222993
> rowMax(tmp5,na.rm=TRUE)
[1] 466.31367 87.32080 81.46000 95.56617 85.08276 91.98516 NA
[8] 89.53594 83.28249 91.66329
> rowMin(tmp5,na.rm=TRUE)
[1] 56.16307 53.21192 58.72573 59.21205 56.76712 56.17240 NA 54.41264
[9] 55.36808 55.68758
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 111.35977 71.04270 71.01799 68.28793 70.99465 76.50185 64.96003
[8] 68.35247 72.36985 73.05648 69.41211 70.16804 NaN 68.12333
[15] 71.40394 73.54745 72.36641 70.75524 70.68557 72.18272
> colSums(tmp5,na.rm=TRUE)
[1] 1002.2379 639.3843 639.1619 614.5914 638.9519 688.5167 584.6403
[8] 615.1722 651.3286 657.5083 624.7090 631.5123 0.0000 613.1100
[15] 642.6354 661.9271 651.2977 636.7972 636.1701 649.6445
> colVars(tmp5,na.rm=TRUE)
[1] 17803.82059 45.91798 58.44837 64.86973 66.70153 110.81033
[7] 47.86825 156.81771 95.89521 77.43291 73.93709 82.90787
[13] NA 59.08256 77.54453 127.27099 38.44755 139.92002
[19] 123.54435 81.52802
> colSd(tmp5,na.rm=TRUE)
[1] 133.430958 6.776281 7.645153 8.054175 8.167100 10.526649
[7] 6.918688 12.522688 9.792610 8.799597 8.598668 9.105376
[13] NA 7.686518 8.805937 11.281445 6.200609 11.828779
[19] 11.115050 9.029287
> colMax(tmp5,na.rm=TRUE)
[1] 466.31367 83.15833 79.49018 84.76259 82.69284 91.66329 73.89881
[8] 95.56617 89.45584 89.53594 83.20591 91.31119 -Inf 80.04744
[15] 85.08276 91.56892 80.14503 89.51778 91.98516 83.28249
> colMin(tmp5,na.rm=TRUE)
[1] 53.21192 57.22988 56.43605 59.93903 58.72573 60.22153 55.36808 55.68758
[9] 56.88135 59.34343 57.79257 60.55080 Inf 59.55385 59.68411 58.16331
[17] 62.73119 54.41264 56.16307 58.09132
>
>
>
>
> 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] 233.0617 236.0685 252.2545 249.4471 181.5094 254.7410 140.5276 404.4860
[9] 182.6223 162.5313
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 233.0617 236.0685 252.2545 249.4471 181.5094 254.7410 140.5276 404.4860
[9] 182.6223 162.5313
>
>
>
> 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] 8.526513e-14 5.684342e-14 -1.136868e-13 -1.989520e-13 -5.684342e-14
[6] -2.273737e-13 1.278977e-13 1.136868e-13 1.136868e-13 -8.526513e-14
[11] 8.526513e-14 1.705303e-13 0.000000e+00 -5.684342e-14 5.684342e-14
[16] -8.526513e-14 -2.842171e-14 6.394885e-14 3.410605e-13 5.684342e-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 14
9 12
6 9
9 1
2 17
7 13
5 16
4 20
1 2
3 3
8 18
5 14
5 13
9 4
1 6
7 20
2 7
3 18
1 2
7 14
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] 2.70173
> Min(tmp)
[1] -2.205203
> mean(tmp)
[1] -0.1127626
> Sum(tmp)
[1] -11.27626
> Var(tmp)
[1] 0.9900849
>
> rowMeans(tmp)
[1] -0.1127626
> rowSums(tmp)
[1] -11.27626
> rowVars(tmp)
[1] 0.9900849
> rowSd(tmp)
[1] 0.9950301
> rowMax(tmp)
[1] 2.70173
> rowMin(tmp)
[1] -2.205203
>
> colMeans(tmp)
[1] -0.58265286 0.27606328 -1.31698155 -0.98720110 -0.59779554 0.49183738
[7] 1.25425111 -0.22356593 -0.63332996 0.12135572 1.53918620 -1.63199980
[13] 0.02142753 0.51532145 1.38610565 0.46234866 1.05804430 -0.23189084
[19] -0.66014012 0.59614666 -0.26872600 -0.46156748 0.15107411 1.10809848
[25] -1.66217388 -0.50031927 -0.45931484 -1.19591594 0.66239891 0.11925447
[31] 0.02476782 0.58775949 0.47202025 0.40294861 -0.53514491 0.49038225
[37] -0.25259703 -1.39224829 0.18020945 -0.57393329 -1.23852683 0.19580959
[43] -0.21185895 1.29606527 -1.77681984 -0.63575888 -0.01131185 -0.10660018
[49] 0.75198407 -1.02461933 0.40512363 -0.50610911 -0.37715307 -1.21349080
[55] 0.08288428 -1.85724576 0.80739001 2.61842410 -0.08400666 1.28816593
[61] -0.67310793 -2.20520282 1.60092875 -0.10337570 -0.03601235 -0.56785166
[67] 0.45869619 -2.03368997 2.30651782 -1.23149099 0.43442112 -1.49185153
[73] 0.10000711 0.49374030 -0.57280903 -0.77586565 -0.86537214 2.70172972
[79] -1.94291505 -0.43173922 1.22271888 0.39906592 0.58617015 -1.09495280
[85] -1.07726337 -1.79398375 -1.01180757 0.67290321 0.95277920 0.43162071
[91] 0.73862421 -0.01405273 0.02348461 -1.24667680 0.58978240 0.80519421
[97] -0.59656332 -0.29019435 -0.60586345 -1.28785371
> colSums(tmp)
[1] -0.58265286 0.27606328 -1.31698155 -0.98720110 -0.59779554 0.49183738
[7] 1.25425111 -0.22356593 -0.63332996 0.12135572 1.53918620 -1.63199980
[13] 0.02142753 0.51532145 1.38610565 0.46234866 1.05804430 -0.23189084
[19] -0.66014012 0.59614666 -0.26872600 -0.46156748 0.15107411 1.10809848
[25] -1.66217388 -0.50031927 -0.45931484 -1.19591594 0.66239891 0.11925447
[31] 0.02476782 0.58775949 0.47202025 0.40294861 -0.53514491 0.49038225
[37] -0.25259703 -1.39224829 0.18020945 -0.57393329 -1.23852683 0.19580959
[43] -0.21185895 1.29606527 -1.77681984 -0.63575888 -0.01131185 -0.10660018
[49] 0.75198407 -1.02461933 0.40512363 -0.50610911 -0.37715307 -1.21349080
[55] 0.08288428 -1.85724576 0.80739001 2.61842410 -0.08400666 1.28816593
[61] -0.67310793 -2.20520282 1.60092875 -0.10337570 -0.03601235 -0.56785166
[67] 0.45869619 -2.03368997 2.30651782 -1.23149099 0.43442112 -1.49185153
[73] 0.10000711 0.49374030 -0.57280903 -0.77586565 -0.86537214 2.70172972
[79] -1.94291505 -0.43173922 1.22271888 0.39906592 0.58617015 -1.09495280
[85] -1.07726337 -1.79398375 -1.01180757 0.67290321 0.95277920 0.43162071
[91] 0.73862421 -0.01405273 0.02348461 -1.24667680 0.58978240 0.80519421
[97] -0.59656332 -0.29019435 -0.60586345 -1.28785371
> 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] -0.58265286 0.27606328 -1.31698155 -0.98720110 -0.59779554 0.49183738
[7] 1.25425111 -0.22356593 -0.63332996 0.12135572 1.53918620 -1.63199980
[13] 0.02142753 0.51532145 1.38610565 0.46234866 1.05804430 -0.23189084
[19] -0.66014012 0.59614666 -0.26872600 -0.46156748 0.15107411 1.10809848
[25] -1.66217388 -0.50031927 -0.45931484 -1.19591594 0.66239891 0.11925447
[31] 0.02476782 0.58775949 0.47202025 0.40294861 -0.53514491 0.49038225
[37] -0.25259703 -1.39224829 0.18020945 -0.57393329 -1.23852683 0.19580959
[43] -0.21185895 1.29606527 -1.77681984 -0.63575888 -0.01131185 -0.10660018
[49] 0.75198407 -1.02461933 0.40512363 -0.50610911 -0.37715307 -1.21349080
[55] 0.08288428 -1.85724576 0.80739001 2.61842410 -0.08400666 1.28816593
[61] -0.67310793 -2.20520282 1.60092875 -0.10337570 -0.03601235 -0.56785166
[67] 0.45869619 -2.03368997 2.30651782 -1.23149099 0.43442112 -1.49185153
[73] 0.10000711 0.49374030 -0.57280903 -0.77586565 -0.86537214 2.70172972
[79] -1.94291505 -0.43173922 1.22271888 0.39906592 0.58617015 -1.09495280
[85] -1.07726337 -1.79398375 -1.01180757 0.67290321 0.95277920 0.43162071
[91] 0.73862421 -0.01405273 0.02348461 -1.24667680 0.58978240 0.80519421
[97] -0.59656332 -0.29019435 -0.60586345 -1.28785371
> colMin(tmp)
[1] -0.58265286 0.27606328 -1.31698155 -0.98720110 -0.59779554 0.49183738
[7] 1.25425111 -0.22356593 -0.63332996 0.12135572 1.53918620 -1.63199980
[13] 0.02142753 0.51532145 1.38610565 0.46234866 1.05804430 -0.23189084
[19] -0.66014012 0.59614666 -0.26872600 -0.46156748 0.15107411 1.10809848
[25] -1.66217388 -0.50031927 -0.45931484 -1.19591594 0.66239891 0.11925447
[31] 0.02476782 0.58775949 0.47202025 0.40294861 -0.53514491 0.49038225
[37] -0.25259703 -1.39224829 0.18020945 -0.57393329 -1.23852683 0.19580959
[43] -0.21185895 1.29606527 -1.77681984 -0.63575888 -0.01131185 -0.10660018
[49] 0.75198407 -1.02461933 0.40512363 -0.50610911 -0.37715307 -1.21349080
[55] 0.08288428 -1.85724576 0.80739001 2.61842410 -0.08400666 1.28816593
[61] -0.67310793 -2.20520282 1.60092875 -0.10337570 -0.03601235 -0.56785166
[67] 0.45869619 -2.03368997 2.30651782 -1.23149099 0.43442112 -1.49185153
[73] 0.10000711 0.49374030 -0.57280903 -0.77586565 -0.86537214 2.70172972
[79] -1.94291505 -0.43173922 1.22271888 0.39906592 0.58617015 -1.09495280
[85] -1.07726337 -1.79398375 -1.01180757 0.67290321 0.95277920 0.43162071
[91] 0.73862421 -0.01405273 0.02348461 -1.24667680 0.58978240 0.80519421
[97] -0.59656332 -0.29019435 -0.60586345 -1.28785371
> colMedians(tmp)
[1] -0.58265286 0.27606328 -1.31698155 -0.98720110 -0.59779554 0.49183738
[7] 1.25425111 -0.22356593 -0.63332996 0.12135572 1.53918620 -1.63199980
[13] 0.02142753 0.51532145 1.38610565 0.46234866 1.05804430 -0.23189084
[19] -0.66014012 0.59614666 -0.26872600 -0.46156748 0.15107411 1.10809848
[25] -1.66217388 -0.50031927 -0.45931484 -1.19591594 0.66239891 0.11925447
[31] 0.02476782 0.58775949 0.47202025 0.40294861 -0.53514491 0.49038225
[37] -0.25259703 -1.39224829 0.18020945 -0.57393329 -1.23852683 0.19580959
[43] -0.21185895 1.29606527 -1.77681984 -0.63575888 -0.01131185 -0.10660018
[49] 0.75198407 -1.02461933 0.40512363 -0.50610911 -0.37715307 -1.21349080
[55] 0.08288428 -1.85724576 0.80739001 2.61842410 -0.08400666 1.28816593
[61] -0.67310793 -2.20520282 1.60092875 -0.10337570 -0.03601235 -0.56785166
[67] 0.45869619 -2.03368997 2.30651782 -1.23149099 0.43442112 -1.49185153
[73] 0.10000711 0.49374030 -0.57280903 -0.77586565 -0.86537214 2.70172972
[79] -1.94291505 -0.43173922 1.22271888 0.39906592 0.58617015 -1.09495280
[85] -1.07726337 -1.79398375 -1.01180757 0.67290321 0.95277920 0.43162071
[91] 0.73862421 -0.01405273 0.02348461 -1.24667680 0.58978240 0.80519421
[97] -0.59656332 -0.29019435 -0.60586345 -1.28785371
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.5826529 0.2760633 -1.316982 -0.9872011 -0.5977955 0.4918374 1.254251
[2,] -0.5826529 0.2760633 -1.316982 -0.9872011 -0.5977955 0.4918374 1.254251
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -0.2235659 -0.63333 0.1213557 1.539186 -1.632 0.02142753 0.5153215
[2,] -0.2235659 -0.63333 0.1213557 1.539186 -1.632 0.02142753 0.5153215
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 1.386106 0.4623487 1.058044 -0.2318908 -0.6601401 0.5961467 -0.268726
[2,] 1.386106 0.4623487 1.058044 -0.2318908 -0.6601401 0.5961467 -0.268726
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -0.4615675 0.1510741 1.108098 -1.662174 -0.5003193 -0.4593148 -1.195916
[2,] -0.4615675 0.1510741 1.108098 -1.662174 -0.5003193 -0.4593148 -1.195916
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.6623989 0.1192545 0.02476782 0.5877595 0.4720202 0.4029486 -0.5351449
[2,] 0.6623989 0.1192545 0.02476782 0.5877595 0.4720202 0.4029486 -0.5351449
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.4903823 -0.252597 -1.392248 0.1802095 -0.5739333 -1.238527 0.1958096
[2,] 0.4903823 -0.252597 -1.392248 0.1802095 -0.5739333 -1.238527 0.1958096
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.211859 1.296065 -1.77682 -0.6357589 -0.01131185 -0.1066002 0.7519841
[2,] -0.211859 1.296065 -1.77682 -0.6357589 -0.01131185 -0.1066002 0.7519841
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -1.024619 0.4051236 -0.5061091 -0.3771531 -1.213491 0.08288428 -1.857246
[2,] -1.024619 0.4051236 -0.5061091 -0.3771531 -1.213491 0.08288428 -1.857246
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 0.80739 2.618424 -0.08400666 1.288166 -0.6731079 -2.205203 1.600929
[2,] 0.80739 2.618424 -0.08400666 1.288166 -0.6731079 -2.205203 1.600929
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] -0.1033757 -0.03601235 -0.5678517 0.4586962 -2.03369 2.306518 -1.231491
[2,] -0.1033757 -0.03601235 -0.5678517 0.4586962 -2.03369 2.306518 -1.231491
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] 0.4344211 -1.491852 0.1000071 0.4937403 -0.572809 -0.7758656 -0.8653721
[2,] 0.4344211 -1.491852 0.1000071 0.4937403 -0.572809 -0.7758656 -0.8653721
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 2.70173 -1.942915 -0.4317392 1.222719 0.3990659 0.5861701 -1.094953
[2,] 2.70173 -1.942915 -0.4317392 1.222719 0.3990659 0.5861701 -1.094953
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] -1.077263 -1.793984 -1.011808 0.6729032 0.9527792 0.4316207 0.7386242
[2,] -1.077263 -1.793984 -1.011808 0.6729032 0.9527792 0.4316207 0.7386242
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -0.01405273 0.02348461 -1.246677 0.5897824 0.8051942 -0.5965633 -0.2901943
[2,] -0.01405273 0.02348461 -1.246677 0.5897824 0.8051942 -0.5965633 -0.2901943
[,99] [,100]
[1,] -0.6058635 -1.287854
[2,] -0.6058635 -1.287854
>
>
> Max(tmp2)
[1] 2.72721
> Min(tmp2)
[1] -2.10906
> mean(tmp2)
[1] 0.0661155
> Sum(tmp2)
[1] 6.61155
> Var(tmp2)
[1] 0.8973857
>
> rowMeans(tmp2)
[1] 0.41073282 0.46591864 -0.58176862 -0.65557187 -0.54307845 1.15743673
[7] -0.15776957 -0.21202107 0.64406042 -1.55379795 0.40020163 0.15217739
[13] 0.20941487 0.40323247 -0.24433241 1.73186977 -0.79921419 -2.10906010
[19] -1.64690395 1.02174123 0.35408506 -1.15249178 -0.36977448 -0.49065833
[25] -0.46585371 2.07892958 -0.54311304 0.67013642 -0.75509121 0.60747991
[31] -0.71465345 -1.16026617 0.33312632 -0.14366580 -0.53518806 1.38064152
[37] -0.46160556 1.26311688 -0.90127386 -1.18694893 2.72721041 0.07201115
[43] 0.57174867 0.42067596 1.86376687 0.99342550 0.92001247 0.91501582
[49] -0.08036167 0.10014270 -1.08121312 0.04069048 -1.28063611 -0.47546894
[55] -0.80822405 2.35621494 0.31374700 -0.72428611 0.53444088 -2.06812410
[61] 1.15541065 0.05497862 -1.87640654 -0.91298377 1.48235427 0.26404991
[67] 1.35649990 0.25302940 -1.00856321 -0.70681830 0.17993657 0.48707526
[73] -0.26809129 0.23870423 -1.45606293 0.24574972 -1.00114132 0.17779511
[79] 0.73973100 -0.50865804 0.39335892 -0.56740408 0.56925795 -0.25369538
[85] -0.04870170 0.68869739 0.97134282 1.44490385 0.21614265 1.13746294
[91] -0.06363180 1.38562181 -0.71391336 0.84804415 -0.03073236 -0.71039876
[97] -0.44194643 0.91762424 0.40072549 0.36121506
> rowSums(tmp2)
[1] 0.41073282 0.46591864 -0.58176862 -0.65557187 -0.54307845 1.15743673
[7] -0.15776957 -0.21202107 0.64406042 -1.55379795 0.40020163 0.15217739
[13] 0.20941487 0.40323247 -0.24433241 1.73186977 -0.79921419 -2.10906010
[19] -1.64690395 1.02174123 0.35408506 -1.15249178 -0.36977448 -0.49065833
[25] -0.46585371 2.07892958 -0.54311304 0.67013642 -0.75509121 0.60747991
[31] -0.71465345 -1.16026617 0.33312632 -0.14366580 -0.53518806 1.38064152
[37] -0.46160556 1.26311688 -0.90127386 -1.18694893 2.72721041 0.07201115
[43] 0.57174867 0.42067596 1.86376687 0.99342550 0.92001247 0.91501582
[49] -0.08036167 0.10014270 -1.08121312 0.04069048 -1.28063611 -0.47546894
[55] -0.80822405 2.35621494 0.31374700 -0.72428611 0.53444088 -2.06812410
[61] 1.15541065 0.05497862 -1.87640654 -0.91298377 1.48235427 0.26404991
[67] 1.35649990 0.25302940 -1.00856321 -0.70681830 0.17993657 0.48707526
[73] -0.26809129 0.23870423 -1.45606293 0.24574972 -1.00114132 0.17779511
[79] 0.73973100 -0.50865804 0.39335892 -0.56740408 0.56925795 -0.25369538
[85] -0.04870170 0.68869739 0.97134282 1.44490385 0.21614265 1.13746294
[91] -0.06363180 1.38562181 -0.71391336 0.84804415 -0.03073236 -0.71039876
[97] -0.44194643 0.91762424 0.40072549 0.36121506
> 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] 0.41073282 0.46591864 -0.58176862 -0.65557187 -0.54307845 1.15743673
[7] -0.15776957 -0.21202107 0.64406042 -1.55379795 0.40020163 0.15217739
[13] 0.20941487 0.40323247 -0.24433241 1.73186977 -0.79921419 -2.10906010
[19] -1.64690395 1.02174123 0.35408506 -1.15249178 -0.36977448 -0.49065833
[25] -0.46585371 2.07892958 -0.54311304 0.67013642 -0.75509121 0.60747991
[31] -0.71465345 -1.16026617 0.33312632 -0.14366580 -0.53518806 1.38064152
[37] -0.46160556 1.26311688 -0.90127386 -1.18694893 2.72721041 0.07201115
[43] 0.57174867 0.42067596 1.86376687 0.99342550 0.92001247 0.91501582
[49] -0.08036167 0.10014270 -1.08121312 0.04069048 -1.28063611 -0.47546894
[55] -0.80822405 2.35621494 0.31374700 -0.72428611 0.53444088 -2.06812410
[61] 1.15541065 0.05497862 -1.87640654 -0.91298377 1.48235427 0.26404991
[67] 1.35649990 0.25302940 -1.00856321 -0.70681830 0.17993657 0.48707526
[73] -0.26809129 0.23870423 -1.45606293 0.24574972 -1.00114132 0.17779511
[79] 0.73973100 -0.50865804 0.39335892 -0.56740408 0.56925795 -0.25369538
[85] -0.04870170 0.68869739 0.97134282 1.44490385 0.21614265 1.13746294
[91] -0.06363180 1.38562181 -0.71391336 0.84804415 -0.03073236 -0.71039876
[97] -0.44194643 0.91762424 0.40072549 0.36121506
> rowMin(tmp2)
[1] 0.41073282 0.46591864 -0.58176862 -0.65557187 -0.54307845 1.15743673
[7] -0.15776957 -0.21202107 0.64406042 -1.55379795 0.40020163 0.15217739
[13] 0.20941487 0.40323247 -0.24433241 1.73186977 -0.79921419 -2.10906010
[19] -1.64690395 1.02174123 0.35408506 -1.15249178 -0.36977448 -0.49065833
[25] -0.46585371 2.07892958 -0.54311304 0.67013642 -0.75509121 0.60747991
[31] -0.71465345 -1.16026617 0.33312632 -0.14366580 -0.53518806 1.38064152
[37] -0.46160556 1.26311688 -0.90127386 -1.18694893 2.72721041 0.07201115
[43] 0.57174867 0.42067596 1.86376687 0.99342550 0.92001247 0.91501582
[49] -0.08036167 0.10014270 -1.08121312 0.04069048 -1.28063611 -0.47546894
[55] -0.80822405 2.35621494 0.31374700 -0.72428611 0.53444088 -2.06812410
[61] 1.15541065 0.05497862 -1.87640654 -0.91298377 1.48235427 0.26404991
[67] 1.35649990 0.25302940 -1.00856321 -0.70681830 0.17993657 0.48707526
[73] -0.26809129 0.23870423 -1.45606293 0.24574972 -1.00114132 0.17779511
[79] 0.73973100 -0.50865804 0.39335892 -0.56740408 0.56925795 -0.25369538
[85] -0.04870170 0.68869739 0.97134282 1.44490385 0.21614265 1.13746294
[91] -0.06363180 1.38562181 -0.71391336 0.84804415 -0.03073236 -0.71039876
[97] -0.44194643 0.91762424 0.40072549 0.36121506
>
> colMeans(tmp2)
[1] 0.0661155
> colSums(tmp2)
[1] 6.61155
> colVars(tmp2)
[1] 0.8973857
> colSd(tmp2)
[1] 0.9473045
> colMax(tmp2)
[1] 2.72721
> colMin(tmp2)
[1] -2.10906
> colMedians(tmp2)
[1] 0.12616
> colRanges(tmp2)
[,1]
[1,] -2.10906
[2,] 2.72721
>
> 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] 2.30298227 -2.32255133 2.04259704 -0.42917651 -2.23181620 0.05914892
[7] 9.13228239 -3.31694610 -3.44832701 0.32634409
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.5616713
[2,] -0.2748417
[3,] 0.3357521
[4,] 0.8862927
[5,] 1.8881277
>
> rowApply(tmp,sum)
[1] -7.4587600 -5.2057579 1.9382713 2.4369232 4.9837225 0.6864639
[7] 2.6049573 1.9864424 2.5047075 -2.3624326
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 6 2 10 8 8 7 5 7 3 6
[2,] 2 8 5 6 4 6 2 6 5 5
[3,] 4 6 9 7 9 10 9 2 1 2
[4,] 7 5 7 3 5 2 4 5 9 4
[5,] 1 10 1 2 3 4 3 8 8 8
[6,] 9 7 2 5 6 8 7 9 2 1
[7,] 10 3 3 9 10 9 10 10 10 7
[8,] 8 9 8 4 2 3 1 1 4 9
[9,] 3 4 4 1 1 1 6 4 7 10
[10,] 5 1 6 10 7 5 8 3 6 3
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 0.676531325 0.045175188 0.407541467 -1.146567537 -1.923897183
[6] -1.435282279 1.469091084 -0.473285815 -1.873902330 1.325330833
[11] -3.431959159 -2.949842960 -0.004635444 1.251303776 -0.560417854
[16] 0.556734074 4.205882012 3.024972758 0.367881495 -2.533546792
> colApply(tmp,quantile)[,1]
[,1]
[1,] -2.1256471
[2,] 0.4360352
[3,] 0.6073696
[4,] 0.6881576
[5,] 1.0706161
>
> rowApply(tmp,sum)
[1] -5.06630077 7.23022454 -0.60961717 0.07901234 -4.63621227
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 17 13 15 16 1
[2,] 7 2 17 15 12
[3,] 18 10 6 14 7
[4,] 6 9 1 19 3
[5,] 4 4 5 12 17
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.4360352 -0.6435463 0.64521961 -0.70468973 -1.2877346 -0.3338983
[2,] 0.6073696 -1.1147511 0.09932336 0.07429173 -0.5839744 0.5426725
[3,] 0.6881576 0.9368961 -0.67632844 -1.18150577 -0.6944156 -0.6132313
[4,] 1.0706161 1.0623305 0.74588455 1.52451653 0.3999667 -0.7360648
[5,] -2.1256471 -0.1957540 -0.40655761 -0.85918030 0.2422606 -0.2947603
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -1.7632005 -1.7052048 -0.5774653 0.140367711 -1.9095293 -0.8545448
[2,] 1.2118621 1.2033072 0.1461906 -0.048448315 -0.2853321 -0.6516550
[3,] 0.9430908 -0.9080477 0.5598619 -0.176613825 -0.1214394 -0.3418001
[4,] 1.3928035 0.7376181 -1.8874752 1.415829985 -0.7244650 -0.5529524
[5,] -0.3154649 0.1990413 -0.1150144 -0.005804723 -0.3911934 -0.5488907
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -0.04397081 -0.1717306 1.2084165 0.1210985 3.12265234 -0.39943053
[2,] -0.28997582 2.1306536 1.2298248 1.6599457 2.19957214 0.02614038
[3,] -1.00755068 0.7065614 -0.8938701 -0.1928035 -0.60682712 1.58495898
[4,] -0.15007736 -1.6921767 -1.1878722 -0.5912736 -0.09736089 1.85733149
[5,] 1.48693923 0.2779961 -0.9169168 -0.4402330 -0.41215445 -0.04402756
[,19] [,20]
[1,] -0.5258749 0.1807296
[2,] 0.7929695 -1.7197618
[3,] 1.0889671 0.2963224
[4,] -1.4250533 -1.0831137
[5,] 0.4368730 -0.2077233
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 655 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 567 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.11-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 -0.5105777 0.7961543 -0.3996326 -0.948839 0.5107592 -0.4482881 -0.8130532
col8 col9 col10 col11 col12 col13 col14
row1 -0.2802163 -1.48536 -0.6712194 -0.9287783 1.592394 -0.5686617 0.5823517
col15 col16 col17 col18 col19 col20
row1 0.04922557 0.08201621 0.401793 -0.7896495 -0.7182934 0.2344872
> tmp[,"col10"]
col10
row1 -0.6712194
row2 -0.5739390
row3 1.5634758
row4 0.4597251
row5 0.2187906
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6
row1 -0.51057766 0.7961543 -0.3996326 -0.9488390 0.5107592 -0.4482881
row5 0.04908677 -0.5024026 1.1060470 -0.7715036 -1.4429180 -0.9112614
col7 col8 col9 col10 col11 col12
row1 -0.81305316 -0.2802163 -1.4853600 -0.6712194 -0.9287783 1.59239436
row5 0.06726633 -0.4631948 -0.1895633 0.2187906 0.3155165 -0.02956141
col13 col14 col15 col16 col17 col18
row1 -0.5686617 0.5823517 0.04922557 0.08201621 0.40179305 -0.7896495
row5 -0.3827639 -0.3386835 0.44247121 1.67303214 0.04404729 -0.6954171
col19 col20
row1 -0.7182934 0.2344872
row5 -1.4711855 1.0495013
> tmp[,c("col6","col20")]
col6 col20
row1 -0.4482881 0.2344872
row2 -1.0869117 -1.2242900
row3 -2.0978527 1.2720771
row4 -1.3402057 0.6012609
row5 -0.9112614 1.0495013
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -0.4482881 0.2344872
row5 -0.9112614 1.0495013
>
>
>
>
> 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 51.50951 50.01057 48.29518 51.20824 51.68849 103.347 49.36598 51.71106
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.21197 49.54806 51.27122 50.28071 49.25322 49.64479 49.18001 49.22566
col17 col18 col19 col20
row1 49.47417 50.54339 51.63792 105.035
> tmp[,"col10"]
col10
row1 49.54806
row2 31.17168
row3 30.24374
row4 27.87730
row5 48.92838
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 51.50951 50.01057 48.29518 51.20824 51.68849 103.347 49.36598 51.71106
row5 49.70260 52.82798 49.07868 49.55542 51.44302 104.413 49.57029 50.04938
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.21197 49.54806 51.27122 50.28071 49.25322 49.64479 49.18001 49.22566
row5 50.20571 48.92838 51.29548 49.61918 50.99012 49.06531 50.24702 50.23847
col17 col18 col19 col20
row1 49.47417 50.54339 51.63792 105.0350
row5 51.01066 49.48594 50.50662 105.7445
> tmp[,c("col6","col20")]
col6 col20
row1 103.34697 105.03496
row2 75.11781 77.14161
row3 75.23518 74.94851
row4 73.83147 74.43747
row5 104.41296 105.74455
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 103.347 105.0350
row5 104.413 105.7445
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 103.347 105.0350
row5 104.413 105.7445
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -0.4989149
[2,] -0.1413962
[3,] -1.2516922
[4,] -2.1848874
[5,] 0.4457931
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.10922781 -0.9753678
[2,] 1.17449841 -0.3003024
[3,] 0.02304149 0.1901590
[4,] 0.18251943 1.6315893
[5,] 1.48080934 0.3462511
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 0.7284608 1.1747543
[2,] 0.6017673 -0.1385683
[3,] 1.1802357 -0.9944322
[4,] 0.7527670 -0.1239602
[5,] -0.0302202 -0.6264092
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 0.7284608
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 0.7284608
[2,] 0.6017673
>
>
>
> 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 -0.4471186 -1.2319188 -1.9008669 -0.42172483 0.3601296 -2.1563551
row1 -0.2547765 0.4390428 0.5610562 0.07695402 0.5299082 0.7792331
[,7] [,8] [,9] [,10] [,11] [,12]
row3 0.8903179 0.05019628 -1.1370471 1.4132642 -1.425282 -0.7496151
row1 1.4761349 1.18549418 0.1036129 -0.5307056 1.130766 -0.9609536
[,13] [,14] [,15] [,16] [,17] [,18] [,19]
row3 0.06291846 1.2591524 0.1338004 1.676181 0.1740052 -1.0450600 1.905759
row1 -2.51027206 -0.3602875 0.3782410 -0.319367 -0.7251661 -0.7612034 -1.317936
[,20]
row3 0.6026891
row1 1.1481636
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.1199246 -0.3919976 -1.553573 0.068769 -0.2757302 -1.30895 -0.4554413
[,8] [,9] [,10]
row2 0.4519168 0.9575353 1.067414
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 1.661612 0.6596418 0.1340303 0.6594741 -0.2183257 -2.046232 2.464833
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.01216409 -1.430123 -1.087246 -0.5972269 -0.3798602 -0.3778846 0.4111773
[,15] [,16] [,17] [,18] [,19] [,20]
row5 0.3394683 1.521659 0.2907343 -1.118556 -0.3791421 2.707059
>
>
> 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: 0x7fd7d5401d80>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM12ef29fa67c8"
[2] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM12ef216b38096"
[3] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM12ef262bf037e"
[4] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM12ef26a7e77d7"
[5] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM12ef214edfae0"
[6] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM12ef213f192dc"
[7] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM12ef258e0b3be"
[8] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM12ef2838ac88"
[9] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM12ef240c718ef"
[10] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM12ef24f361422"
[11] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM12ef26763ecce"
[12] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM12ef2514ffd69"
[13] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM12ef25a862233"
[14] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM12ef21c2f70b3"
[15] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM12ef26e900639"
>
>
> ### 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: 0x7fd7e03100e0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x7fd7e03100e0>
Warning message:
In dir.create(new.directory) :
'/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x7fd7e03100e0>
> rowMedians(tmp)
[1] -0.068043606 0.327058972 0.036334060 0.354742136 0.687384437
[6] -0.369001028 -0.079886885 0.140266579 0.421357722 0.743310114
[11] 0.326464976 -0.313854947 -0.188946021 -0.059853506 0.068299966
[16] -0.070439558 -0.214874992 0.333199875 0.398330437 0.049226968
[21] -0.260099299 -0.121541766 -0.605079423 0.012920131 -0.512487747
[26] 0.547090101 -0.178189536 0.146632650 -0.231532457 -0.371180003
[31] 0.596492861 0.273679261 0.584548519 -0.045660149 -0.017520105
[36] 0.013136871 -0.067975305 -0.497337402 0.097970817 -0.315022010
[41] 0.377375876 -0.250525919 0.342550434 0.230581243 -0.132476308
[46] -0.079932526 0.202135953 -0.242194453 0.104536655 -0.296044771
[51] 0.314639380 -0.067276207 -0.007758307 0.201948013 -0.294665769
[56] -0.399105609 -0.250515912 -0.005839530 -0.303682349 0.210793813
[61] 0.008451439 -0.515753121 -0.155373303 0.027417527 0.088043908
[66] -0.231445989 -0.296052986 -0.327552434 -0.104819620 0.352021386
[71] -0.588577614 -0.076395452 -0.113929730 0.002664981 -0.852593436
[76] 0.650915258 0.020782469 -0.187161617 0.345338375 -0.093240048
[81] -0.788239393 0.250942824 -0.178133153 -0.266298829 0.151098716
[86] -0.291716965 -0.221175259 0.139306790 0.445878249 0.043059528
[91] 0.401725935 0.300475480 -0.675621222 0.023173145 -0.001677925
[96] 0.013185041 0.270536154 -0.086013149 0.481156405 -0.301526701
[101] -0.108109155 0.322705137 0.017728190 -0.185033146 0.110004527
[106] 0.205267942 0.046092577 -0.439736378 0.022161327 -0.049068994
[111] 0.087892743 -0.543756861 0.272084649 -0.675454070 -0.084668936
[116] -0.162387391 0.265429453 0.127474900 -0.189233360 -0.074286403
[121] 0.196904805 0.004984437 0.261959481 -0.435138353 0.551237053
[126] -0.784331137 -0.747504302 -0.052748578 0.264384861 -0.271572571
[131] 0.285370255 0.041008989 0.167765033 0.330926712 -0.609754237
[136] -0.189812401 0.030048406 -0.493848606 -0.157565895 -0.318270065
[141] 0.066779022 0.514851308 0.281873902 -0.420241195 -0.712973368
[146] -0.059035441 -0.359769503 -0.234405748 -0.086224484 -0.785580269
[151] 0.083875630 -0.208373027 -0.290518665 0.225248357 -0.254749787
[156] 0.689764216 -0.092731828 0.084605785 0.111135925 -0.052542727
[161] -0.282800968 -1.095025180 -0.568334087 -0.306694704 0.158453983
[166] -0.395702109 0.415022124 0.113216742 0.781800253 0.140631830
[171] 0.791342270 -0.434362622 0.117287570 0.155124968 -0.268941602
[176] -0.048418983 0.149176103 -0.705145723 0.404491470 0.489461699
[181] 0.333988323 0.035143084 0.037573575 -0.279952321 -0.195652389
[186] -0.305918341 -0.212892726 0.118455073 0.049814574 -0.569023403
[191] -0.185846264 -0.139322098 0.232886779 0.475937264 -0.097336060
[196] -0.310024823 -0.505990050 -0.193463747 0.116164880 -0.510062583
[201] 0.298442420 0.141219055 0.372359965 0.040991482 -0.106856335
[206] 0.202195676 0.076486096 0.015644970 0.259912144 -0.174365629
[211] -0.519822006 0.036579846 -0.131782838 0.103580065 0.400008612
[216] 0.339684262 0.062441191 -0.265440222 -0.152272056 0.004101997
[221] 0.350877361 0.300973907 0.016147829 0.071578745 0.555524387
[226] -0.214351071 0.028284338 0.260615392 -0.101824684 -0.155600245
>
> proc.time()
user system elapsed
3.905 12.105 16.278
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
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: 0x7f9f615282e0>
> .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: 0x7f9f615282e0>
> .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: 0x7f9f615282e0>
> .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: 0x7f9f615282e0>
> 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: 0x7f9f1171c8d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x7f9f1171c8d0>
> .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: 0x7f9f1171c8d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x7f9f1171c8d0>
> .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: 0x7f9f1171c8d0>
> 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: 0x7f9f115068d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x7f9f115068d0>
> .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: 0x7f9f115068d0>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x7f9f115068d0>
> .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: 0x7f9f115068d0>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x7f9f115068d0>
> .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: 0x7f9f115068d0>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x7f9f115068d0>
> .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: 0x7f9f115068d0>
> 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: 0x7f9f13100000>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x7f9f13100000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x7f9f13100000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x7f9f13100000>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile130a7649f1d0c" "BufferedMatrixFile130a7a2c3270"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile130a7649f1d0c" "BufferedMatrixFile130a7a2c3270"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x7f9f13100350>
> .Call("R_bm_AddColumn",P)
<pointer: 0x7f9f13100350>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x7f9f13100350>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x7f9f13100350>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x7f9f13100350>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x7f9f13100350>
> .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: 0x7f9f51414f30>
> .Call("R_bm_AddColumn",P)
<pointer: 0x7f9f51414f30>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x7f9f51414f30>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x7f9f51414f30>
> 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: 0x7f9f13200090>
> .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: 0x7f9f13200090>
> rm(P)
>
> proc.time()
user system elapsed
0.523 0.142 0.641
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
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
0.487 0.086 0.548