J. Toedling
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/girafe |
| Branch: RELEASE_3_12 |
| Last Commit: 983e1ff |
| Last Changed Date: 2020-10-27 10:37:50 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:31:30 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the girafe package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 743/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| girafe 1.42.0 (landing page) J. Toedling
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: girafe |
| Version: 1.42.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:girafe.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings girafe_1.42.0.tar.gz |
| StartedAt: 2021-05-06 03:14:43 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 03:21:41 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 418.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: girafe.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:girafe.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings girafe_1.42.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/girafe.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.42.0'
* 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-3.12-bioc/tmpdir/RtmpctpO9i/R.INSTALL1568703d7dfc/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-3.12-bioc/tmpdir/RtmpctpO9i/R.INSTALL1568703d7dfc/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-3.12-bioc/tmpdir/RtmpctpO9i/R.INSTALL1568703d7dfc/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-3.12-bioc/tmpdir/RtmpctpO9i/R.INSTALL1568703d7dfc/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-3.12-bioc/tmpdir/RtmpctpO9i/R.INSTALL1568703d7dfc/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-3.12-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 : <anonymous>: no visible global function definition for
'IRangesList'
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'
coverage,AlignedGenomeIntervals : <anonymous>: 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-3.12-bioc/R/library/girafe/libs/i386/girafe.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-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 (user + system) or elapsed time > 5s
user system elapsed
AlignedGenomeIntervals-class 17.48 1.19 19.20
negbinomsig 14.35 1.57 16.37
perWindow 13.26 0.42 13.69
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
perWindow 15.36 0.46 15.88
negbinomsig 14.49 0.43 14.90
AlignedGenomeIntervals-class 12.73 0.87 13.66
* 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-3.12-bioc/meat/girafe.Rcheck/00check.log'
for details.
girafe.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/girafe_1.42.0.tar.gz && rm -rf girafe.buildbin-libdir && mkdir girafe.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=girafe.buildbin-libdir girafe_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL girafe_1.42.0.zip && rm girafe_1.42.0.tar.gz girafe_1.42.0.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 1061k 100 1061k 0 0 3862k 0 --:--:-- --:--:-- --:--:-- 3872k
install for i386
* installing *source* package 'girafe' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c coverage.cpp -o coverage.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c girafe_init.c -o girafe_init.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -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-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-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 requests: 'score', 'score<-', '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-3.12-bioc/tmpdir/RtmpctpO9i/R.INSTALL1568703d7dfc/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-3.12-bioc/tmpdir/RtmpctpO9i/R.INSTALL1568703d7dfc/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-3.12-bioc/tmpdir/RtmpctpO9i/R.INSTALL1568703d7dfc/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-3.12-bioc/tmpdir/RtmpctpO9i/R.INSTALL1568703d7dfc/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-3.12-bioc/tmpdir/RtmpctpO9i/R.INSTALL1568703d7dfc/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 requests: 'score', 'score<-', 'sort' when loading 'girafe'
** testing if installed package can be loaded from final location
No methods found in package 'IRanges' for requests: 'score', 'score<-', 'sort' when loading 'girafe'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'girafe' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c coverage.cpp -o coverage.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c girafe_init.c -o girafe_init.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -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-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/girafe.buildbin-libdir/girafe/libs/x64
** testing if installed package can be loaded
No methods found in package 'IRanges' for requests: 'score', 'score<-', 'sort' when loading 'girafe'
* MD5 sums
packaged installation of 'girafe' as girafe_1.42.0.zip
* DONE (girafe)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'girafe' successfully unpacked and MD5 sums checked
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girafe.Rcheck/examples_i386/girafe-Ex.timings
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girafe.Rcheck/examples_x64/girafe-Ex.timings
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