J. Toedling
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/girafe |
| Branch: RELEASE_3_6 |
| Last Commit: a087188 |
| Last Changed Date: 2017-10-30 12:39:29 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:20:08 -0400 (Thu, 12 Apr 2018).
| Package 586/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| girafe 1.30.0 J. Toedling
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: girafe |
| Version: 1.30.0 |
| Command: rm -rf girafe.buildbin-libdir girafe.Rcheck && mkdir girafe.buildbin-libdir girafe.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=girafe.buildbin-libdir girafe_1.30.0.tar.gz >girafe.Rcheck\00install.out 2>&1 && cp girafe.Rcheck\00install.out girafe-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=girafe.buildbin-libdir --install="check:girafe-install.out" --force-multiarch --no-vignettes --timings girafe_1.30.0.tar.gz |
| StartedAt: 2018-04-12 00:25:11 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 00:31:24 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 373.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: girafe.Rcheck |
| Warnings: 1 |
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### Running command:
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### rm -rf girafe.buildbin-libdir girafe.Rcheck && mkdir girafe.buildbin-libdir girafe.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=girafe.buildbin-libdir girafe_1.30.0.tar.gz >girafe.Rcheck\00install.out 2>&1 && cp girafe.Rcheck\00install.out girafe-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=girafe.buildbin-libdir --install="check:girafe-install.out" --force-multiarch --no-vignettes --timings girafe_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/girafe.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.30.0'
* 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-3.6-bioc/tmpdir/RtmpeqQ8cq/R.INSTALLc0c163e5160/girafe/man/fracOverlap.Rd:38: missing file link 'interval_overlap'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpeqQ8cq/R.INSTALLc0c163e5160/girafe/man/trimAdapter.Rd:39: missing file link 'narrow'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpeqQ8cq/R.INSTALLc0c163e5160/girafe/man/trimAdapter.Rd:41: missing file link 'writeFastq'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpeqQ8cq/R.INSTALLc0c163e5160/girafe/man/weightedConsensusMatrix.Rd:23: missing file link 'consensusMatrix'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpeqQ8cq/R.INSTALLc0c163e5160/girafe/man/whichNearestMethods.Rd:44: missing file link 'which_nearest'
See 'C:/Users/biocbuild/bbs-3.6-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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 : <anonymous>: no visible global function definition for
'RangesList'
agiFromBam : <anonymous>: no visible global function definition for
'scanBamFlag'
agiFromBam : <anonymous>: 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'
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'
reduce,RangedData: no visible binding for global variable 'rd'
Undefined global functions or variables:
DNAString Index1 RangesList ScanBamParam Views alphabetFrequency
fraction1 fraction2 mclapply n.reads narrow rd 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 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-3.6-bioc/meat/girafe.buildbin-libdir/girafe/libs/i386/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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
negbinomsig 9.27 0.34 9.61
perWindow 8.93 0.38 9.31
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
negbinomsig 12.63 0.34 12.97
perWindow 10.56 0.39 10.96
AlignedGenomeIntervals-class 6.48 0.86 7.36
* 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-3.6-bioc/meat/girafe.Rcheck/00check.log'
for details.
girafe.Rcheck/00install.out
install for i386
* installing *source* package 'girafe' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=generic -c coverage.cpp -o coverage.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/girafe.buildbin-libdir/girafe/libs/i386
** R
** inst
** preparing 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-3.6-bioc/tmpdir/RtmpeqQ8cq/R.INSTALLc0c163e5160/girafe/man/fracOverlap.Rd:38: missing file link 'interval_overlap'
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-3.6-bioc/tmpdir/RtmpeqQ8cq/R.INSTALLc0c163e5160/girafe/man/trimAdapter.Rd:39: missing file link 'narrow'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpeqQ8cq/R.INSTALLc0c163e5160/girafe/man/trimAdapter.Rd:41: missing file link 'writeFastq'
weightedConsensusMatrix html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpeqQ8cq/R.INSTALLc0c163e5160/girafe/man/weightedConsensusMatrix.Rd:23: missing file link 'consensusMatrix'
whichNearestMethods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpeqQ8cq/R.INSTALLc0c163e5160/girafe/man/whichNearestMethods.Rd:44: missing file link 'which_nearest'
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package 'IRanges' for request: 'sort' when loading 'girafe'
In R CMD INSTALL
install for x64
* installing *source* package 'girafe' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=generic -c coverage.cpp -o coverage.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/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:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-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_1.30.0.zip
* DONE (girafe)
In R CMD INSTALL
In R CMD INSTALL
|
girafe.Rcheck/examples_i386/girafe-Ex.timings
|
girafe.Rcheck/examples_x64/girafe-Ex.timings
|