Peter Hickey
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/DelayedMatrixStats |
| Branch: RELEASE_3_8 |
| Last Commit: eb5b390 |
| Last Changed Date: 2018-10-30 11:42:06 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:28:28 -0400 (Sat, 13 Apr 2019).
| Package 389/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DelayedMatrixStats 1.4.0 Peter Hickey
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: DelayedMatrixStats |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DelayedMatrixStats.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DelayedMatrixStats_1.4.0.tar.gz |
| StartedAt: 2019-04-13 01:42:38 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 02:08:10 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 1532.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: DelayedMatrixStats.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DelayedMatrixStats.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DelayedMatrixStats_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/DelayedMatrixStats.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DelayedMatrixStats/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DelayedMatrixStats' version '1.4.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 whether package 'DelayedMatrixStats' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colAlls.Rd:70: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colAnyNAs.Rd:53: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colAvgsPerRowSet.Rd:59: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colCollapse.Rd:45: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colCollapse.Rd:83: file link '[' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colCounts.Rd:51: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colCummaxs.Rd:87: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colCummaxs.Rd:131: file link 'cumprod' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colCummaxs.Rd:132: file link 'cummin' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colCummaxs.Rd:132: file link 'cummax' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colDiffs.Rd:51: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colIQRDiffs.Rd:117: file link 'var' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colIQRDiffs.Rd:108: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colIQRDiffs.Rd:172: file link 'var' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colIQRs.Rd:41: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colLogSumExps.Rd:49: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colMads.Rd:73: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colMeans2.Rd:59: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colMedians.Rd:47: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colOrderStats.Rd:46: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colProds.Rd:52: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colProds.Rd:78: file link 'is.nan' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colQuantiles.Rd:55: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colRanks.Rd:53: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colSums2.Rd:59: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colTabulates.Rd:42: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colVars.Rd:51: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colWeightedMads.Rd:59: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colWeightedMeans.Rd:47: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colWeightedMedians.Rd:47: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colWeightedVars.Rd:66: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colWeightedVars.Rd:107: file link 'var' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colsum-HDF5Matrix-method.Rd:61: file link 'HDF5Matrix' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colsum-HDF5Matrix-method.Rd:18: file link 'HDF5Matrix-class' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colsum-HDF5Matrix-method.Rd:34: file link 'getHDF5DumpFile' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colsum-HDF5Matrix-method.Rd:43: file link 'getHDF5DumpChunkDim' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colsum-HDF5Matrix-method.Rd:46: file link 'getHDF5DumpCompressionLevel' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colsum-HDF5Matrix-method.Rd:47: file link 'getHDF5DumpCompressionLevel' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colsum.Rd:77: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/rowsum-DelayedMatrix-method.Rd:36: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/rowsum-DelayedMatrix-method.Rd:12: file link 'DelayedMatrix-class' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/rowsum-DelayedMatrix-method.Rd:29: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/DelayedMatrixStats.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 ... OK
* 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
Missing objects imported by ':::' calls:
'DelayedArray:::.execute_delayed_ops'
'DelayedArray:::get_Nindex_names_along'
Unexported objects imported by ':::' calls:
'DelayedArray:::.get_ans_type'
'DelayedArray:::.reduce_array_dimensions'
'DelayedArray:::RleArraySeed' 'DelayedArray:::colblock_APPLY'
'DelayedArray:::get_Nindex_lengths'
'DelayedArray:::get_verbose_block_processing'
'DelayedArray:::set_dim' 'DelayedArray:::set_dimnames'
'DelayedArray:::subset_by_Nindex' 'DelayedArray:::to_linear_index'
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 ... OK
* checking Rd files ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
colsum-HDF5Matrix-method 0.11 0.06 7.82
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
colsum-HDF5Matrix-method 0.15 0 5.61
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.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: 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/DelayedMatrixStats.Rcheck/00check.log'
for details.
DelayedMatrixStats.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/DelayedMatrixStats_1.4.0.tar.gz && rm -rf DelayedMatrixStats.buildbin-libdir && mkdir DelayedMatrixStats.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DelayedMatrixStats.buildbin-libdir DelayedMatrixStats_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL DelayedMatrixStats_1.4.0.zip && rm DelayedMatrixStats_1.4.0.tar.gz DelayedMatrixStats_1.4.0.zip
###
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% 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 57444 100 57444 0 0 1187k 0 --:--:-- --:--:-- --:--:-- 1304k
install for i386
* installing *source* package 'DelayedMatrixStats' ...
** R
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'rowsum' in package 'DelayedMatrixStats'
** help
*** installing help indices
converting help for package 'DelayedMatrixStats'
finding HTML links ... done
DelayedMatrixStats html
colAlls html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colAlls.Rd:70: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
colAnyNAs html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colAnyNAs.Rd:53: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
colAvgsPerRowSet html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colAvgsPerRowSet.Rd:59: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
colCollapse html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colCollapse.Rd:45: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colCollapse.Rd:83: file link '[' in package 'base' does not exist and so has been treated as a topic
colCounts html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colCounts.Rd:51: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
colCummaxs html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colCummaxs.Rd:87: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colCummaxs.Rd:131: file link 'cumprod' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colCummaxs.Rd:132: file link 'cummin' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colCummaxs.Rd:132: file link 'cummax' in package 'base' does not exist and so has been treated as a topic
colDiffs html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colDiffs.Rd:51: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
colIQRDiffs html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colIQRDiffs.Rd:117: file link 'var' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colIQRDiffs.Rd:108: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colIQRDiffs.Rd:172: file link 'var' in package 'stats' does not exist and so has been treated as a topic
colIQRs html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colIQRs.Rd:41: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
colLogSumExps html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colLogSumExps.Rd:49: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
colMads html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colMads.Rd:73: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
colMeans2 html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colMeans2.Rd:59: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
colMedians html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colMedians.Rd:47: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
colOrderStats html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colOrderStats.Rd:46: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
colProds html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colProds.Rd:52: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colProds.Rd:78: file link 'is.nan' in package 'base' does not exist and so has been treated as a topic
colQuantiles html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colQuantiles.Rd:55: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
colRanks html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colRanks.Rd:53: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
colSums2 html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colSums2.Rd:59: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
colTabulates html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colTabulates.Rd:42: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
colVars html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colVars.Rd:51: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
colWeightedMads html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colWeightedMads.Rd:59: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
colWeightedMeans html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colWeightedMeans.Rd:47: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
colWeightedMedians html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colWeightedMedians.Rd:47: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
colWeightedVars html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colWeightedVars.Rd:66: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colWeightedVars.Rd:107: file link 'var' in package 'stats' does not exist and so has been treated as a topic
colsum-HDF5Matrix-method html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colsum-HDF5Matrix-method.Rd:61: file link 'HDF5Matrix' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colsum-HDF5Matrix-method.Rd:18: file link 'HDF5Matrix-class' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colsum-HDF5Matrix-method.Rd:34: file link 'getHDF5DumpFile' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colsum-HDF5Matrix-method.Rd:43: file link 'getHDF5DumpChunkDim' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colsum-HDF5Matrix-method.Rd:46: file link 'getHDF5DumpCompressionLevel' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colsum-HDF5Matrix-method.Rd:47: file link 'getHDF5DumpCompressionLevel' in package 'HDF5Array' does not exist and so has been treated as a topic
colsum html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/colsum.Rd:77: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
from_DelayedArray_to_simple_seed_class
html
rowblock_APPLY html
rowsum-DelayedMatrix-method html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/rowsum-DelayedMatrix-method.Rd:36: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/rowsum-DelayedMatrix-method.Rd:12: file link 'DelayedMatrix-class' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOOM9h6/R.INSTALL19b8295d15be/DelayedMatrixStats/man/rowsum-DelayedMatrix-method.Rd:29: file link 'getAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
seedClass html
subset_by_Nindex html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'DelayedMatrixStats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DelayedMatrixStats' as DelayedMatrixStats_1.4.0.zip
* DONE (DelayedMatrixStats)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'DelayedMatrixStats' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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DelayedMatrixStats.Rcheck/tests_i386/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> library(testthat)
> library(DelayedMatrixStats)
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
Attaching package: 'DelayedMatrixStats'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyMissings, colAnyNAs, colAnys, colAvgsPerRowSet,
colCollapse, colCounts, colCummaxs, colCummins, colCumprods,
colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps,
colMadDiffs, colMads, colMeans2, colMedians, colOrderStats,
colProds, colQuantiles, colRanks, colSdDiffs, colSds, colSums2,
colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyMissings, rowAnyNAs, rowAnys,
rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins,
rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs,
rowLogSumExps, rowMadDiffs, rowMads, rowMeans2, rowMedians,
rowOrderStats, rowProds, rowQuantiles, rowRanks, rowSdDiffs,
rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
The following object is masked from 'package:base':
rowsum
>
> test_check("DelayedMatrixStats")
Loading required package: rhdf5
== testthat results ===========================================================
OK: 15138 SKIPPED: 1 FAILED: 0
> setAutoBlockSize(8)
automatic block size set to 8 bytes (was 1e+08)
> test_check("DelayedMatrixStats")
== testthat results ===========================================================
OK: 15132 SKIPPED: 1 FAILED: 0
>
> proc.time()
user system elapsed
550.89 5.43 611.15
|
DelayedMatrixStats.Rcheck/tests_x64/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> library(testthat)
> library(DelayedMatrixStats)
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
Attaching package: 'DelayedMatrixStats'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyMissings, colAnyNAs, colAnys, colAvgsPerRowSet,
colCollapse, colCounts, colCummaxs, colCummins, colCumprods,
colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps,
colMadDiffs, colMads, colMeans2, colMedians, colOrderStats,
colProds, colQuantiles, colRanks, colSdDiffs, colSds, colSums2,
colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyMissings, rowAnyNAs, rowAnys,
rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins,
rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs,
rowLogSumExps, rowMadDiffs, rowMads, rowMeans2, rowMedians,
rowOrderStats, rowProds, rowQuantiles, rowRanks, rowSdDiffs,
rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
The following object is masked from 'package:base':
rowsum
>
> test_check("DelayedMatrixStats")
Loading required package: rhdf5
== testthat results ===========================================================
OK: 15138 SKIPPED: 1 FAILED: 0
> setAutoBlockSize(8)
automatic block size set to 8 bytes (was 1e+08)
> test_check("DelayedMatrixStats")
== testthat results ===========================================================
OK: 15132 SKIPPED: 1 FAILED: 0
>
> proc.time()
user system elapsed
657.73 4.92 718.01
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DelayedMatrixStats.Rcheck/examples_i386/DelayedMatrixStats-Ex.timings
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DelayedMatrixStats.Rcheck/examples_x64/DelayedMatrixStats-Ex.timings
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