genomeIntervals 1.25.3
Julien Gagneur
| Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genomeIntervals | | Last Changed Rev: 106408 / Revision: 107602 | | Last Changed Date: 2015-07-15 03:59:08 -0700 (Wed, 15 Jul 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf genomeIntervals.buildbin-libdir genomeIntervals.Rcheck && mkdir genomeIntervals.buildbin-libdir genomeIntervals.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomeIntervals.buildbin-libdir genomeIntervals_1.25.3.tar.gz >genomeIntervals.Rcheck\00install.out 2>&1 && cp genomeIntervals.Rcheck\00install.out genomeIntervals-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=genomeIntervals.buildbin-libdir --install="check:genomeIntervals-install.out" --force-multiarch --no-vignettes --timings genomeIntervals_1.25.3.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/genomeIntervals.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'genomeIntervals/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genomeIntervals' version '1.25.3'
* 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 'genomeIntervals' 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
interval_complement,Genome_intervals : .local: warning in
factor(rep(as.character(fac.comb[, 2]), times = nrows), level =
levels(seqnames(x))): partial argument match of 'level' to 'levels'
interval_complement,Genome_intervals_stranded : .local: warning in
factor(rep(names(s), times = sapply(gi.list, nrow)), level =
levels(strand(x))): partial argument match of 'level' to 'levels'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [8s] OK
** running examples for arch 'x64' ... [8s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'benchmarking-tests.R' [6s]
Comparing 'benchmarking-tests.Rout' to 'benchmarking-tests.Rout.save' ...13,34d12
<
< 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, xtabs
<
< The following objects are masked from 'package:base':
<
< Filter, Find, Map, Position, Reduce, anyDuplicated, append,
< as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
< eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
< mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
< rank, rbind, rep.int, rownames, sapply, setdiff, sort, table,
< tapply, union, unique, unlist, unsplit
<
Running 'consistency-tests.R' [7s]
Running 'fullShow.R' [0s]
Warning message:
running command '"diff" -bw "D:\biocbld\bbs-3.2-bioc\tmpdir\Rtmps1XFSn\Rdiffa1a947ba75fb" "D:\biocbld\bbs-3.2-bioc\tmpdir\Rtmps1XFSn\Rdiffb1a945378656c"' had status 1
[15s] OK
** running tests for arch 'x64' ...
Running 'benchmarking-tests.R' [7s]
Comparing 'benchmarking-tests.Rout' to 'benchmarking-tests.Rout.save' ...13,34d12
<
< 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, xtabs
<
< The following objects are masked from 'package:base':
<
< Filter, Find, Map, Position, Reduce, anyDuplicated, append,
< as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
< eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
< mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
< rank, rbind, rep.int, rownames, sapply, setdiff, sort, table,
< tapply, union, unique, unlist, unsplit
<
Running 'consistency-tests.R' [9s]
Running 'fullShow.R' [0s]
Warning message:
running command '"diff" -bw "D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpQtu28Q\Rdiffa9e46c34689" "D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpQtu28Q\Rdiffb9e450312a3e"' had status 1
[18s] 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 NOTE
See
'D:/biocbld/bbs-3.2-bioc/meat/genomeIntervals.Rcheck/00check.log'
for details.