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CHECK report for girafe on tokay2

This page was generated on 2019-10-16 12:23:34 -0400 (Wed, 16 Oct 2019).

Package 680/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
girafe 1.36.0
J. Toedling
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/girafe
Branch: RELEASE_3_9
Last Commit: 6696c01
Last Changed Date: 2019-05-02 11:53:13 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: girafe
Version: 1.36.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:girafe.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings girafe_1.36.0.tar.gz
StartedAt: 2019-10-16 04:04:54 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:11:21 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 386.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: girafe.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:girafe.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings girafe_1.36.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/girafe.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'girafe/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'girafe' version '1.36.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'S4Vectors', 'Rsamtools', 'intervals', 'ShortRead',
  'genomeIntervals', 'grid'
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 'girafe' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSmmPcf/R.INSTALL207c6a3218b/girafe/man/fracOverlap.Rd:38: file link 'interval_overlap' in package 'genomeIntervals' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSmmPcf/R.INSTALL207c6a3218b/girafe/man/trimAdapter.Rd:39: file link 'narrow' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSmmPcf/R.INSTALL207c6a3218b/girafe/man/trimAdapter.Rd:41: file link 'writeFastq' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSmmPcf/R.INSTALL207c6a3218b/girafe/man/weightedConsensusMatrix.Rd:23: file link 'consensusMatrix' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSmmPcf/R.INSTALL207c6a3218b/girafe/man/whichNearestMethods.Rd:44: file link 'which_nearest' in package 'intervals' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/girafe.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'genomeIntervals'
A package should be listed in only one of these fields.
* 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
'library' or 'require' call to 'MASS' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'Rsamtools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'genomeIntervals:::intervalsForOverlap'
  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
agiFromBam: no visible binding for global variable 'mclapply'
agiFromBam: no visible global function definition for 'scanBamHeader'
agiFromBam: no visible global function definition for 'ScanBamParam'
agiFromBam : : no visible global function definition for
  'IRangesList'
agiFromBam : : no visible global function definition for
  'scanBamFlag'
agiFromBam : : no visible global function definition for
  'scanBam'
countReadsAnnotated: no visible binding for global variable 'mclapply'
countReadsAnnotated: no visible binding for global variable 'fraction1'
fracOverlap: no visible binding for global variable 'fraction1'
fracOverlap: no visible binding for global variable 'fraction2'
getFeatureCounts: no visible binding for global variable 'fraction1'
getFeatureCounts: no visible binding for global variable 'Index1'
intPhred: no visible binding for global variable 'mclapply'
oldAGIoverlap: no visible binding for global variable 'mclapply'
plotReads: no visible binding for global variable 'x.start'
plotReads: no visible binding for global variable 'x.end'
plotReads: no visible binding for global variable 'y'
reduceOne: no visible binding for global variable 'fraction1'
reduceOne: no visible binding for global variable 'fraction2'
trimAdapter: no visible global function definition for 'DNAString'
trimAdapter: no visible global function definition for 'narrow'
windowCountAndGC: no visible binding for global variable 'n.reads'
windowCountAndGC: no visible global function definition for 'Views'
windowCountAndGC: no visible global function definition for 'unmasked'
windowCountAndGC: no visible global function definition for
  'alphabetFrequency'
clusters,AlignedGenomeIntervals: no visible binding for global variable
  'mclapply'
clusters,Genome_intervals: no visible binding for global variable
  'mclapply'
coverage,AlignedGenomeIntervals: no visible binding for global variable
  'mclapply'
coverage,AlignedGenomeIntervals : : no visible binding for
  global variable 'on.minus'
interval_included,AlignedGenomeIntervals-AlignedGenomeIntervals: no
  visible binding for global variable 'mclapply'
reduce,AlignedGenomeIntervals: no visible binding for global variable
  'mclapply'
reduce,Genome_intervals: no visible binding for global variable
  'mclapply'
reduce,Genome_intervals: no visible binding for global variable
  'fraction1'
reduce,Genome_intervals: no visible binding for global variable
  'fraction2'
Undefined global functions or variables:
  DNAString IRangesList Index1 ScanBamParam Views alphabetFrequency
  fraction1 fraction2 mclapply n.reads narrow on.minus scanBam
  scanBamFlag scanBamHeader unmasked x.end x.start y
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/girafe/libs/i386/girafe.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/girafe/libs/x64/girafe.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
AlignedGenomeIntervals-class 14.75   0.97   16.14
perWindow                     9.78   0.34   10.12
negbinomsig                   9.16   0.44    9.59
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
negbinomsig                  16.22   0.71   16.95
AlignedGenomeIntervals-class 14.92   1.38   16.31
perWindow                    13.93   0.38   14.31
* 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, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/girafe.Rcheck/00check.log'
for details.

Installation output

girafe.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/girafe_1.36.0.tar.gz && rm -rf girafe.buildbin-libdir && mkdir girafe.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=girafe.buildbin-libdir girafe_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL girafe_1.36.0.zip && rm girafe_1.36.0.tar.gz girafe_1.36.0.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 1062k  100 1062k    0     0  14.3M      0 --:--:-- --:--:-- --:--:-- 15.9M

install for i386

* installing *source* package 'girafe' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c coverage.cpp -o coverage.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c girafe_init.c -o girafe_init.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o girafe.dll tmp.def coverage.o girafe_init.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/girafe.buildbin-libdir/00LOCK-girafe/00new/girafe/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'IRanges' for request: 'sort' when loading 'girafe'
Creating a generic function for 'sample' from package 'base' in package 'girafe'
** help
*** installing help indices
  converting help for package 'girafe'
    finding HTML links ... done
    AlignedGenomeIntervals-class            html  
    agiFromBam                              html  
    countReadsAnnotated                     html  
    fracOverlap                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSmmPcf/R.INSTALL207c6a3218b/girafe/man/fracOverlap.Rd:38: file link 'interval_overlap' in package 'genomeIntervals' does not exist and so has been treated as a topic
    getFeatureCounts                        html  
    girafe-internal                         html  
    intPhred                                html  
    medianByPosition                        html  
    negbinomsig                             html  
    perWindow                               html  
    plotAligned                             html  
    plotReads                               html  
    plotnegbinomfit                         html  
    reduce-extras                           html  
    trimAdapter                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSmmPcf/R.INSTALL207c6a3218b/girafe/man/trimAdapter.Rd:39: file link 'narrow' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSmmPcf/R.INSTALL207c6a3218b/girafe/man/trimAdapter.Rd:41: file link 'writeFastq' in package 'ShortRead' does not exist and so has been treated as a topic
    weightedConsensusMatrix                 html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSmmPcf/R.INSTALL207c6a3218b/girafe/man/weightedConsensusMatrix.Rd:23: file link 'consensusMatrix' in package 'Biostrings' does not exist and so has been treated as a topic
    whichNearestMethods                     html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSmmPcf/R.INSTALL207c6a3218b/girafe/man/whichNearestMethods.Rd:44: file link 'which_nearest' in package 'intervals' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'IRanges' for request: 'sort' when loading 'girafe'
** testing if installed package can be loaded from final location
No methods found in package 'IRanges' for request: 'sort' when loading 'girafe'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'girafe' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c coverage.cpp -o coverage.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c girafe_init.c -o girafe_init.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o girafe.dll tmp.def coverage.o girafe_init.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/girafe.buildbin-libdir/girafe/libs/x64
** testing if installed package can be loaded
No methods found in package 'IRanges' for request: 'sort' when loading 'girafe'
* MD5 sums
packaged installation of 'girafe' as girafe_1.36.0.zip
* DONE (girafe)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'girafe' successfully unpacked and MD5 sums checked

Tests output

Example timings

girafe.Rcheck/examples_i386/girafe-Ex.timings

nameusersystemelapsed
AlignedGenomeIntervals-class14.75 0.9716.14
agiFromBam0.330.000.33
countReadsAnnotated0.130.000.12
fracOverlap0.250.000.25
intPhred0.280.410.91
medianByPosition0.640.371.02
negbinomsig9.160.449.59
perWindow 9.78 0.3410.12
plotAligned0.010.000.02
trimAdapter0.290.380.66
weightedConsensusMatrix000
whichNearestMethods0.500.230.73

girafe.Rcheck/examples_x64/girafe-Ex.timings

nameusersystemelapsed
AlignedGenomeIntervals-class14.92 1.3816.31
agiFromBam0.350.000.34
countReadsAnnotated0.170.000.17
fracOverlap0.250.000.25
intPhred0.330.410.74
medianByPosition0.720.391.11
negbinomsig16.22 0.7116.95
perWindow13.93 0.3814.31
plotAligned0.030.000.04
trimAdapter0.320.230.54
weightedConsensusMatrix000
whichNearestMethods0.590.330.92