Hervé Pagès
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/DelayedArray |
| Branch: RELEASE_3_7 |
| Last Commit: bdb0ac0 |
| Last Changed Date: 2018-09-10 18:06:18 -0400 (Mon, 10 Sep 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:43:14 -0400 (Wed, 17 Oct 2018).
| Package 365/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DelayedArray 0.6.6 Hervé Pagès
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: DelayedArray |
| Version: 0.6.6 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DelayedArray.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings DelayedArray_0.6.6.tar.gz |
| StartedAt: 2018-10-17 01:30:37 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 01:43:53 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 796.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: DelayedArray.Rcheck |
| Warnings: 3 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DelayedArray.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings DelayedArray_0.6.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/DelayedArray.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DelayedArray/DESCRIPTION' ... OK
* this is package 'DelayedArray' version '0.6.6'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'stats4' 'matrixStats' 'BiocGenerics' 'S4Vectors' 'IRanges'
'BiocParallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 whether package 'DelayedArray' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-class.Rd:119: file link 'HDF5Array' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-class.Rd:203: file link 'HDF5Array' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-class.Rd:205: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-stats.Rd:60: file link 'dnorm' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-stats.Rd:60: file link 'dbinom' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-stats.Rd:61: file link 'dpois' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-stats.Rd:61: file link 'dlogis' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-stats.Rd:68: file link 'dnorm' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-stats.Rd:68: file link 'dbinom' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-stats.Rd:69: file link 'dpois' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-stats.Rd:69: file link 'dlogis' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-stats.Rd:75: file link 'HDF5Array' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:99: file link 'Ops' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:100: file link 'Math' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:100: file link 'Math2' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:119: file link 'Summary' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:133: file link 'is.na' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:133: file link '!' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:135: file link '%*%' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:138: file link 'rowSums' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:139: file link 'rowMaxs' in package 'matrixStats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:155: file link 'HDF5Array' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:158: file link 'Ops' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:159: file link 'Math' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:159: file link 'Math2' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/RleArray-class.Rd:68: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/RleArray-class.Rd:91: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/RleArray-class.Rd:101: file link 'HDF5Array' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/RleArray-class.Rd:103: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/bind-arrays.Rd:40: file link 'rbind' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/extract_array.Rd:46: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/extract_array.Rd:103: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/realize.Rd:79: file link 'HDF5Array' in package 'HDF5Array' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/DelayedArray.Rcheck/00install.out' for details.
* 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 ... WARNING
Subdirectory 'inst/doc' contains invalid file names:
'02-Implementing_a_backend.Rmd' '01-Working_with_large_arrays.Rnw'
'02-Implementing_a_backend.html' '01-Working_with_large_arrays.pdf'
Please remove or rename the files.
See section 'Package subdirectories' in the 'Writing R Extensions'
manual.
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Unexported objects imported by ':::' calls:
'BiocGenerics:::replaceSlots' 'BiocGenerics:::testPackage'
'S4Vectors:::anyMissing' 'S4Vectors:::anyMissingOrOutside'
'S4Vectors:::diffWithInitialZero'
'S4Vectors:::extract_positions_from_Rle' 'S4Vectors:::sapply_isNULL'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
block_MAPPLY: no visible binding for global variable 'x'
Undefined global functions or variables:
x
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'blockApply' 'currentBlockId' 'currentViewport' 'defaultGrid'
'effectiveGrid'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
DelayedArray-utils 5.08 1.23 6.31
DelayedArray-class 5.36 0.41 7.02
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
DelayedArray-class 5.22 0.33 5.65
DelayedArray-utils 4.46 1.05 5.51
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'run_unitTests.R'
OK
** running tests for arch 'x64' ...
Running 'run_unitTests.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: 3 WARNINGs, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/DelayedArray.Rcheck/00check.log'
for details.
DelayedArray.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/DelayedArray_0.6.6.tar.gz && rm -rf DelayedArray.buildbin-libdir && mkdir DelayedArray.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DelayedArray.buildbin-libdir DelayedArray_0.6.6.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL DelayedArray_0.6.6.zip && rm DelayedArray_0.6.6.tar.gz DelayedArray_0.6.6.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 78128 100 78128 0 0 1283k 0 --:--:-- --:--:-- --:--:-- 1467k
install for i386
* installing *source* package 'DelayedArray' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'aperm' in package 'DelayedArray'
in method for 'coerce' with signature '"DelayedMatrix","dgCMatrix"': no definition for class "dgCMatrix"
in method for 'coerce' with signature '"DelayedMatrix","sparseMatrix"': no definition for class "sparseMatrix"
Creating a generic function for 'sweep' from package 'base' in package 'DelayedArray'
Creating a new generic function for 'apply' in package 'DelayedArray'
Creating a generic function for 'dnorm' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'pnorm' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'qnorm' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'dbinom' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'pbinom' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'qbinom' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'dpois' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'ppois' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'qpois' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'dlogis' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'plogis' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'qlogis' from package 'stats' in package 'DelayedArray'
Creating a new generic function for 'rowMaxs' in package 'DelayedArray'
Creating a new generic function for 'colMaxs' in package 'DelayedArray'
Creating a new generic function for 'rowMins' in package 'DelayedArray'
Creating a new generic function for 'colMins' in package 'DelayedArray'
Creating a new generic function for 'rowRanges' in package 'DelayedArray'
Creating a new generic function for 'colRanges' in package 'DelayedArray'
** help
*** installing help indices
converting help for package 'DelayedArray'
finding HTML links ... done
Array-class html
ArrayGrid-class html
DelayedArray-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-class.Rd:119: file link 'HDF5Array' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-class.Rd:203: file link 'HDF5Array' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-class.Rd:205: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
DelayedArray-stats html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-stats.Rd:60: file link 'dnorm' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-stats.Rd:60: file link 'dbinom' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-stats.Rd:61: file link 'dpois' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-stats.Rd:61: file link 'dlogis' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-stats.Rd:68: file link 'dnorm' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-stats.Rd:68: file link 'dbinom' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-stats.Rd:69: file link 'dpois' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-stats.Rd:69: file link 'dlogis' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-stats.Rd:75: file link 'HDF5Array' in package 'HDF5Array' does not exist and so has been treated as a topic
DelayedArray-utils html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:99: file link 'Ops' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:100: file link 'Math' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:100: file link 'Math2' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:119: file link 'Summary' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:133: file link 'is.na' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:133: file link '!' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:135: file link '%*%' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:138: file link 'rowSums' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:139: file link 'rowMaxs' in package 'matrixStats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:155: file link 'HDF5Array' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:158: file link 'Ops' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:159: file link 'Math' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/DelayedArray-utils.Rd:159: file link 'Math2' in package 'methods' does not exist and so has been treated as a topic
DelayedOp-class html
RleArray-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/RleArray-class.Rd:68: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/RleArray-class.Rd:91: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/RleArray-class.Rd:101: file link 'HDF5Array' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/RleArray-class.Rd:103: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
bind-arrays html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/bind-arrays.Rd:40: file link 'rbind' in package 'base' does not exist and so has been treated as a topic
block_processing html
extract_array html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/extract_array.Rd:46: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/extract_array.Rd:103: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
realize html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGpHtE/R.INSTALLef44904192f/DelayedArray/man/realize.Rd:79: file link 'HDF5Array' in package 'HDF5Array' does not exist and so has been treated as a topic
showtree html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'DelayedArray' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DelayedArray' as DelayedArray_0.6.6.zip
* DONE (DelayedArray)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'DelayedArray' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
DelayedArray.Rcheck/tests_i386/run_unitTests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.
> require("DelayedArray") || stop("unable to load DelayedArray package")
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply
[1] TRUE
> DelayedArray:::.test()
Attaching package: 'genefilter'
The following objects are masked from 'package:matrixStats':
rowSds, rowVars
RUNIT TEST PROTOCOL -- Wed Oct 17 01:37:39 2018
***********************************************
Number of test functions: 25
Number of errors: 0
Number of failures: 0
1 Test Suite :
DelayedArray RUnit Tests - 25 test functions, 0 errors, 0 failures
Number of test functions: 25
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
287.06 4.39 291.84
|
DelayedArray.Rcheck/tests_x64/run_unitTests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
> require("DelayedArray") || stop("unable to load DelayedArray package")
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply
[1] TRUE
> DelayedArray:::.test()
Attaching package: 'genefilter'
The following objects are masked from 'package:matrixStats':
rowSds, rowVars
RUNIT TEST PROTOCOL -- Wed Oct 17 01:43:47 2018
***********************************************
Number of test functions: 25
Number of errors: 0
Number of failures: 0
1 Test Suite :
DelayedArray RUnit Tests - 25 test functions, 0 errors, 0 failures
Number of test functions: 25
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
363.12 4.23 368.03
|
|
DelayedArray.Rcheck/examples_i386/DelayedArray-Ex.timings
|
DelayedArray.Rcheck/examples_x64/DelayedArray-Ex.timings
|