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This page was generated on 2022-04-13 12:08:05 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for girafe on machv2


To the developers/maintainers of the girafe package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/girafe.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 783/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
girafe 1.46.0  (landing page)
J. Toedling
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/girafe
git_branch: RELEASE_3_14
git_last_commit: 4803e9e
git_last_commit_date: 2021-10-26 11:55:45 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: girafe
Version: 1.46.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:girafe.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings girafe_1.46.0.tar.gz
StartedAt: 2022-04-12 13:52:08 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 13:57:22 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 314.9 seconds
RetCode: 0
Status:   OK  
CheckDir: girafe.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:girafe.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings girafe_1.46.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/girafe.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.46.0’
* 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 : <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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
negbinomsig                  14.139  0.158  14.308
perWindow                    14.119  0.115  14.247
AlignedGenomeIntervals-class  9.197  0.174   9.380
* 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-3.14-bioc/meat/girafe.Rcheck/00check.log’
for details.



Installation output

girafe.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL girafe
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘girafe’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c girafe_init.c -o girafe_init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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/4.1/Resources/library/00LOCK-girafe/00new/girafe/libs
** 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
** 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’
** 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 requests: ‘score’, ‘score<-’, ‘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-class9.1970.1749.380
agiFromBam0.2970.0040.302
countReadsAnnotated0.1320.0010.134
fracOverlap0.2990.0060.306
intPhred0.2670.3680.639
medianByPosition0.7480.0880.836
negbinomsig14.139 0.15814.308
perWindow14.119 0.11514.247
plotAligned0.0310.0000.031
trimAdapter0.1840.0620.246
weightedConsensusMatrix0.0060.0000.006
whichNearestMethods0.4820.0700.555