R453Plus1Toolbox 1.16.0
Hans-Ulrich Klein
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/R453Plus1Toolbox | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
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### Running command:
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### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings R453Plus1Toolbox_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘R453Plus1Toolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘R453Plus1Toolbox’ version ‘1.16.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘R453Plus1Toolbox’ can be installed ... [31s/31s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ‘BSgenome.Hsapiens.UCSC.hg19’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.annotateVariants_MapperSet: no visible binding for global variable
‘Hsapiens’
.ava2vcf: no visible global function definition for ‘getSeq’
.ava2vcf: no visible binding for global variable ‘Hsapiens’
.ava2vcf: no visible global function definition for ‘DataFrame’
.ava2vcf: no visible global function definition for ‘DataFrameList’
.ava2vcf: no visible global function definition for ‘SimpleList’
.ava2vcf: no visible global function definition for ‘Rle’
.ava2vcf: no visible global function definition for ‘CharacterList’
.baseFrequency: no visible global function definition for
‘alphabetFrequency’
.complexity.dust: no visible global function definition for
‘trinucleotideFrequency’
.complexity.entropy: no visible global function definition for
‘trinucleotideFrequency’
.detectBreakpoints: no visible binding for global variable ‘Hsapiens’
.dinucleotideOddsRatio: no visible global function definition for
‘dinucleotideFrequency’
.dinucleotideOddsRatio: no visible global function definition for
‘oligonucleotideFrequency’
.filterChimericReads: no visible global function definition for
‘elementLengths’
.gcContent: no visible global function definition for
‘alphabetFrequency’
.gcContentHist: no visible global function definition for
‘alphabetFrequency’
.getEnsemblInfo: no visible binding for global variable ‘cds_length’
.getEnsemblInfo: no visible binding for global variable
‘ensembl_transcript_id’
.getMutations: no visible binding for global variable ‘PatternStart’
.getMutations: no visible binding for global variable ‘PatternEnd’
.htmlReport: no visible binding for global variable ‘VarFreqForward’
.htmlReport: no visible binding for global variable ‘VarFreqReverse’
.plotVariants: no visible binding for global variable ‘mutation’
qualityReportSFF: no visible binding for '<<-' assignment to ‘tmp’
readSFF: no visible global function definition for ‘PhredQuality’
readSFF: no visible global function definition for
‘QualityScaledDNAStringSet’
addRead,SFFContainer-SFFRead: no visible global function definition for
‘PhredQuality’
addRead,SFFContainer-SFFRead: no visible global function definition for
‘QualityScaledDNAStringSet’
annotateVariants,MapperSet-BSgenome: no visible binding for global
variable ‘Hsapiens’
annotateVariants,MapperSet-missing: no visible binding for global
variable ‘Hsapiens’
ava2vcf,AVASet: no visible global function definition for ‘getSeq’
ava2vcf,AVASet: no visible binding for global variable ‘Hsapiens’
ava2vcf,AVASet: no visible global function definition for ‘DataFrame’
ava2vcf,AVASet: no visible global function definition for
‘DataFrameList’
ava2vcf,AVASet: no visible global function definition for ‘SimpleList’
ava2vcf,AVASet: no visible global function definition for ‘Rle’
ava2vcf,AVASet: no visible global function definition for
‘CharacterList’
baseFrequency,DNAStringSet: no visible global function definition for
‘alphabetFrequency’
complexity.dust,DNAStringSet: no visible global function definition for
‘trinucleotideFrequency’
complexity.entropy,DNAStringSet: no visible global function definition
for ‘trinucleotideFrequency’
detectBreakpoints,list: no visible binding for global variable
‘Hsapiens’
dinucleotideOddsRatio,DNAStringSet: no visible global function
definition for ‘dinucleotideFrequency’
dinucleotideOddsRatio,DNAStringSet: no visible global function
definition for ‘oligonucleotideFrequency’
filterChimericReads,list-RangesList-DNAString-missing-missing: no
visible global function definition for ‘elementLengths’
filterChimericReads,list-RangesList-DNAString-numeric-numeric: no
visible global function definition for ‘elementLengths’
filterChimericReads,list-RangesList-missing-missing-missing: no visible
global function definition for ‘elementLengths’
filterChimericReads,list-RangesList-missing-numeric-numeric: no visible
global function definition for ‘elementLengths’
filterChimericReads,list-missing-DNAString-missing-missing: no visible
global function definition for ‘elementLengths’
filterChimericReads,list-missing-DNAString-numeric-numeric: no visible
global function definition for ‘elementLengths’
filterChimericReads,list-missing-missing-missing-missing: no visible
global function definition for ‘elementLengths’
filterChimericReads,list-missing-missing-numeric-numeric: no visible
global function definition for ‘elementLengths’
gcContent,DNAStringSet: no visible global function definition for
‘alphabetFrequency’
gcContentHist,DNAStringSet: no visible global function definition for
‘alphabetFrequency’
sff2fastq,SFFContainer: no visible global function definition for
‘writeXStringSet’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [35s/36s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mergeBreakpoints 6.248 0.116 6.68
* 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
NOTE: There were 2 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’
for details.
* installing *source* package ‘R453Plus1Toolbox’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c readSFF.c -o readSFF.o
readSFF.c: In function ‘readSFF’:
readSFF.c:46:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c writeSFF.c -o writeSFF.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o R453Plus1Toolbox.so readSFF.o writeSFF.o -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-bioc/meat/R453Plus1Toolbox.Rcheck/R453Plus1Toolbox/libs
** R
** data
** inst
** preparing package for lazy loading
No methods found in "IRanges" for requests: %in%, levels, paste, sapply, substr, substring
No methods found in "Biostrings" for requests: countIndex
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "IRanges" for requests: %in%, levels, paste, sapply, substr, substring
No methods found in "Biostrings" for requests: countIndex
* DONE (R453Plus1Toolbox)