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CHECK report for girafe on celaya2

This page was generated on 2019-10-16 12:48:00 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:girafe.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings girafe_1.36.0.tar.gz
StartedAt: 2019-10-16 03:15:59 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:22:34 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 395.2 seconds
RetCode: 0
Status:  OK 
CheckDir: girafe.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:girafe.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings girafe_1.36.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/girafe.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘girafe’ can be installed ... OK
* 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
* 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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
perWindow                    23.398  0.099  24.721
negbinomsig                  20.329  0.522  20.851
AlignedGenomeIntervals-class 11.194  1.100   9.312
* 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: 5 NOTEs
See
  ‘/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:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL girafe
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘girafe’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c coverage.cpp -o coverage.o
coverage.cpp:2:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c girafe_init.c -o girafe_init.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o girafe.so coverage.o girafe_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-girafe/00new/girafe/libs
** 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
** 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’
** checking absolute paths in shared objects and dynamic libraries
** 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
* DONE (girafe)

Tests output


Example timings

girafe.Rcheck/girafe-Ex.timings

nameusersystemelapsed
AlignedGenomeIntervals-class11.194 1.100 9.312
agiFromBam0.5650.3810.602
countReadsAnnotated0.2400.1030.316
fracOverlap0.3250.0620.387
intPhred0.1850.1400.294
medianByPosition0.8980.3961.180
negbinomsig20.329 0.52220.851
perWindow23.398 0.09924.721
plotAligned0.0490.0010.049
trimAdapter0.1190.0060.131
weightedConsensusMatrix0.0080.0010.009
whichNearestMethods0.4370.0140.502