Peter Hickey
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/DelayedMatrixStats |
| Branch: RELEASE_3_7 |
| Last Commit: de868e7 |
| Last Changed Date: 2018-04-30 10:35:48 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:44:48 -0400 (Wed, 17 Oct 2018).
| Package 366/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DelayedMatrixStats 1.2.0 Peter Hickey
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: DelayedMatrixStats |
| Version: 1.2.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DelayedMatrixStats.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings DelayedMatrixStats_1.2.0.tar.gz |
| StartedAt: 2018-10-17 01:30:49 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 02:00:46 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 1796.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: DelayedMatrixStats.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DelayedMatrixStats.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings DelayedMatrixStats_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/DelayedMatrixStats.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 'DelayedMatrixStats/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'DelayedMatrixStats' version '1.2.0' * package encoding: UTF-8 * 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 whether package 'DelayedMatrixStats' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0Wcxdj/R.INSTALL143421b72808/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-3.7-bioc/tmpdir/Rtmp0Wcxdj/R.INSTALL143421b72808/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-3.7-bioc/tmpdir/Rtmp0Wcxdj/R.INSTALL143421b72808/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-3.7-bioc/tmpdir/Rtmp0Wcxdj/R.INSTALL143421b72808/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-3.7-bioc/tmpdir/Rtmp0Wcxdj/R.INSTALL143421b72808/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-3.7-bioc/tmpdir/Rtmp0Wcxdj/R.INSTALL143421b72808/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-3.7-bioc/tmpdir/Rtmp0Wcxdj/R.INSTALL143421b72808/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-3.7-bioc/tmpdir/Rtmp0Wcxdj/R.INSTALL143421b72808/DelayedMatrixStats/man/colWeightedVars.Rd:107: file link 'var' in package 'stats' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.7-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:::.as_array_or_matrix' 'DelayedArray:::.get_ans_type' 'DelayedArray:::.reduce_array_dimensions' 'DelayedArray:::RleArraySeed' 'DelayedArray:::colblock_APPLY' 'DelayedArray:::extract_block' 'DelayedArray:::get_Nindex_lengths' 'DelayedArray:::get_max_block_length' 'DelayedArray:::get_spacings_for_capped_length_blocks' '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 ** running examples for arch 'x64' ... OK * 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-3.7-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://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/DelayedMatrixStats_1.2.0.tar.gz && rm -rf DelayedMatrixStats.buildbin-libdir && mkdir DelayedMatrixStats.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DelayedMatrixStats.buildbin-libdir DelayedMatrixStats_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL DelayedMatrixStats_1.2.0.zip && rm DelayedMatrixStats_1.2.0.tar.gz DelayedMatrixStats_1.2.0.zip
###
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install for i386
* installing *source* package 'DelayedMatrixStats' ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'DelayedMatrixStats'
finding HTML links ... done
DelayedMatrixStats html
colAlls html
finding level-2 HTML links ... done
colAnyNAs html
colAvgsPerRowSet html
colCollapse html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0Wcxdj/R.INSTALL143421b72808/DelayedMatrixStats/man/colCollapse.Rd:83: file link '[' in package 'base' does not exist and so has been treated as a topic
colCounts html
colCummaxs html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0Wcxdj/R.INSTALL143421b72808/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-3.7-bioc/tmpdir/Rtmp0Wcxdj/R.INSTALL143421b72808/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-3.7-bioc/tmpdir/Rtmp0Wcxdj/R.INSTALL143421b72808/DelayedMatrixStats/man/colCummaxs.Rd:132: file link 'cummax' in package 'base' does not exist and so has been treated as a topic
colDiffs html
colIQRDiffs html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0Wcxdj/R.INSTALL143421b72808/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-3.7-bioc/tmpdir/Rtmp0Wcxdj/R.INSTALL143421b72808/DelayedMatrixStats/man/colIQRDiffs.Rd:172: file link 'var' in package 'stats' does not exist and so has been treated as a topic
colIQRs html
colLogSumExps html
colMads html
colMeans2 html
colMedians html
colOrderStats html
colProds html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0Wcxdj/R.INSTALL143421b72808/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
colRanks html
colSums2 html
colTabulates html
colVars html
colWeightedMads html
colWeightedMeans html
colWeightedMedians html
colWeightedVars html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0Wcxdj/R.INSTALL143421b72808/DelayedMatrixStats/man/colWeightedVars.Rd:107: file link 'var' in package 'stats' does not exist and so has been treated as a topic
from_DelayedArray_to_simple_seed_class
html
rowblock_APPLY html
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_1.2.0.zip
* DONE (DelayedMatrixStats)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-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 3.5.1 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.
> 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
>
> test_check("DelayedMatrixStats")
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Loading required package: rhdf5
== testthat results ===========================================================
OK: 9860 SKIPPED: 0 FAILED: 0
> options(DelayedArray.block.size = 8L)
> test_check("DelayedMatrixStats")
== testthat results ===========================================================
OK: 9860 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
706.92 2.28 709.48
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DelayedMatrixStats.Rcheck/tests_x64/testthat.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.
> 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
>
> test_check("DelayedMatrixStats")
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Loading required package: rhdf5
== testthat results ===========================================================
OK: 9860 SKIPPED: 0 FAILED: 0
> options(DelayedArray.block.size = 8L)
> test_check("DelayedMatrixStats")
== testthat results ===========================================================
OK: 9860 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
941.98 2.62 949.07
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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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