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BioC 3.4: CHECK report for genomeIntervals on moscato1

This page was generated on 2016-09-21 03:42:43 -0700 (Wed, 21 Sep 2016).

Package 491/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genomeIntervals 1.29.0
Julien Gagneur
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genomeIntervals
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: genomeIntervals
Version: 1.29.0
Command: rm -rf genomeIntervals.buildbin-libdir genomeIntervals.Rcheck && mkdir genomeIntervals.buildbin-libdir genomeIntervals.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomeIntervals.buildbin-libdir genomeIntervals_1.29.0.tar.gz >genomeIntervals.Rcheck\00install.out 2>&1 && cp genomeIntervals.Rcheck\00install.out genomeIntervals-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=genomeIntervals.buildbin-libdir --install="check:genomeIntervals-install.out" --force-multiarch --no-vignettes --timings genomeIntervals_1.29.0.tar.gz
StartedAt: 2016-09-20 09:05:25 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 09:08:08 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 162.5 seconds
RetCode: 0
Status:  OK  
CheckDir: genomeIntervals.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf genomeIntervals.buildbin-libdir genomeIntervals.Rcheck && mkdir genomeIntervals.buildbin-libdir genomeIntervals.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomeIntervals.buildbin-libdir genomeIntervals_1.29.0.tar.gz >genomeIntervals.Rcheck\00install.out 2>&1 && cp genomeIntervals.Rcheck\00install.out genomeIntervals-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=genomeIntervals.buildbin-libdir --install="check:genomeIntervals-install.out" --force-multiarch --no-vignettes --timings genomeIntervals_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/genomeIntervals.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.29.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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: 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: warning in
  factor(rep(names(s), times = sapply(gi.list, nrow)), level =
  levels(strand(x))): partial argument match of 'level' to 'levels'
coerce,Genome_intervals-RangedData: no visible global function
  definition for 'na.omit'
writeGff3,data.frame: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  na.omit write.table
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* 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' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'benchmarking-tests.R'
  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, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union,
<     unique, unsplit, which, which.max, which.min
< 
  Running 'consistency-tests.R'
  Running 'fullShow.R'
Warning message:
running command '"diff" -bw "D:\biocbld\bbs-3.4-bioc\tmpdir\RtmpWATuzk\Rdiffa22e0e3275c6" "D:\biocbld\bbs-3.4-bioc\tmpdir\RtmpWATuzk\Rdiffb22e04941b66"' had status 1 
 OK
** running tests for arch 'x64' ...
  Running 'benchmarking-tests.R'
  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, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union,
<     unique, unsplit, which, which.max, which.min
< 
  Running 'consistency-tests.R'
  Running 'fullShow.R'
Warning message:
running command '"diff" -bw "D:\biocbld\bbs-3.4-bioc\tmpdir\RtmpKiG2WP\Rdiffa18043aef74ac" "D:\biocbld\bbs-3.4-bioc\tmpdir\RtmpKiG2WP\Rdiffb180444db3c04"' had status 1 
 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-3.4-bioc/meat/genomeIntervals.Rcheck/00check.log'
for details.


genomeIntervals.Rcheck/00install.out:


install for i386

* installing *source* package 'genomeIntervals' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'genomeIntervals' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genomeIntervals' as genomeIntervals_1.29.0.zip
* DONE (genomeIntervals)

genomeIntervals.Rcheck/examples_i386/genomeIntervals-Ex.timings:

nameusersystemelapsed
GenomeIntervals-constructor0.030.010.05
Genome_intervals-class0.040.000.04
Genome_intervals-coercion-methods000
Genome_intervals-ordering0.070.020.08
Genome_intervals_stranded-class0.040.000.05
c.Genome_intervals0.080.000.08
core_annotated0.030.000.03
distance_to_nearest-methods0.160.000.15
genomeIntervals-readGff30.620.230.86
getGffAttribute0.030.000.03
interval_overlap-methods0.110.000.11
interval_set_operations-methods0.560.000.56
parseGffAttributes0.030.000.04

genomeIntervals.Rcheck/examples_x64/genomeIntervals-Ex.timings:

nameusersystemelapsed
GenomeIntervals-constructor0.080.000.08
Genome_intervals-class0.050.000.05
Genome_intervals-coercion-methods000
Genome_intervals-ordering0.080.000.07
Genome_intervals_stranded-class0.060.000.07
c.Genome_intervals0.060.010.20
core_annotated0.050.000.05
distance_to_nearest-methods0.170.000.25
genomeIntervals-readGff30.660.190.84
getGffAttribute0.050.000.05
interval_overlap-methods0.110.000.11
interval_set_operations-methods0.680.000.69
parseGffAttributes0.030.000.03