girafe 1.25.0
J. Toedling
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/girafe | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings girafe_1.25.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/girafe.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.25.0’
* 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 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’
medianByPosition: no visible binding for global variable ‘median’
oldAGIoverlap: no visible binding for global variable ‘mclapply’
plotAllChrom: no visible global function definition for ‘par’
plotAllChrom: no visible global function definition for ‘abline’
plotAllChrom: no visible global function definition for ‘axTicks’
plotAllChrom: no visible global function definition for ‘points’
plotAllChrom: no visible global function definition for ‘text’
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 abline
alphabetFrequency axTicks fraction1 fraction2 mclapply median n.reads
narrow par points rd scanBam scanBamFlag scanBamHeader text unmasked
x.end x.start y
Consider adding
importFrom("graphics", "abline", "axTicks", "par", "points", "text")
importFrom("stats", "median")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'AlignedGenomeIntervals,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
negbinomsig 9.344 0.012 9.355
perWindow 9.204 0.008 9.212
* 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, 4 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/girafe.Rcheck/00check.log’
for details.
* installing *source* package ‘girafe’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c coverage.cpp -o coverage.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c girafe_init.c -o girafe_init.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o girafe.so coverage.o girafe_init.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/girafe.Rcheck/girafe/libs
** R
** inst
** preparing package for lazy loading
No methods found in "IRanges" for requests: sort
Creating a generic function for ‘hist’ from package ‘graphics’ in package ‘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
No methods found in "IRanges" for requests: sort
* DONE (girafe)