cnvGSA 1.18.0
Joseph Lugo
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/cnvGSA | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf cnvGSA.buildbin-libdir cnvGSA.Rcheck && mkdir cnvGSA.buildbin-libdir cnvGSA.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cnvGSA.buildbin-libdir cnvGSA_1.18.0.tar.gz >cnvGSA.Rcheck\00install.out 2>&1 && cp cnvGSA.Rcheck\00install.out cnvGSA-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=cnvGSA.buildbin-libdir --install="check:cnvGSA-install.out" --force-multiarch --no-vignettes --timings cnvGSA_1.18.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/cnvGSA.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cnvGSA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cnvGSA' version '1.18.0'
* 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 whether package 'cnvGSA' can be installed ... 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
* 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
Packages in Depends field not imported from:
'brglm' 'doParallel' 'foreach' 'splitstackshape'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cnvGSAgsTables: no visible global function definition for 'detectCores'
cnvGSAgsTables: no visible binding for global variable 'SID'
cnvGSAgsTables: no visible binding for global variable 'geneID_TYPE'
cnvGSAgsTables: no visible binding for global variable 'SubjCnvKey'
cnvGSAgsTables: no visible global function definition for
'registerDoParallel'
cnvGSAgsTables: no visible global function definition for '%dopar%'
cnvGSAgsTables: no visible global function definition for 'foreach'
cnvGSAgsTables: no visible binding for global variable 'i'
cnvGSAgsTables: no visible binding for global variable 'CHR'
cnvGSAgsTables: no visible binding for global variable 'BP1'
cnvGSAgsTables: no visible binding for global variable 'BP2'
cnvGSAgsTables: no visible binding for global variable 'TYPE'
cnvGSAgsTables: no visible binding for global variable 'geneID'
cnvGSAgsTables: no visible binding for global variable 'Symbol'
cnvGSAgsTables: no visible binding for global variable 'Symbol_TYPE'
cnvGSAgsTables: no visible binding for global variable 'GsKey'
cnvGSAlogRegTest: no visible binding for global variable 'GsID'
cnvGSAlogRegTest: no visible binding for global variable 'GsKey'
cnvGSAlogRegTest: no visible binding for global variable 'OlpKL_SID'
cnvGSAlogRegTest : f.testGLM_wrap: no visible binding for global
variable 'Condition'
cnvGSAlogRegTest : f.testGLM_wrap: no visible global function
definition for 'detectCores'
cnvGSAlogRegTest : f.testGLM_wrap: no visible global function
definition for 'registerDoParallel'
cnvGSAlogRegTest : f.testGLM_wrap: no visible global function
definition for '%dopar%'
cnvGSAlogRegTest : f.testGLM_wrap: no visible global function
definition for 'foreach'
cnvGSAlogRegTest : f.testGLM_wrap: no visible binding for global
variable 'i'
cnvGSAlogRegTest : f.testGLM_unit: no visible global function
definition for 'glm'
cnvGSAlogRegTest : f.testGLM_unit: no visible global function
definition for 'as.formula'
cnvGSAlogRegTest : f.testGLM_unit: no visible global function
definition for 'binomial'
cnvGSAlogRegTest : f.testGLM_unit: no visible binding for global
variable 'logit'
cnvGSAlogRegTest : f.testGLM_unit: no visible global function
definition for 'anova'
cnvGSAlogRegTest: no visible global function definition for 'p.adjust'
cnvGSAlogRegTest: no visible global function definition for
'write.table'
f.enrProcess: no visible global function definition for 'write.table'
f.makeViz: no visible global function definition for 'write.table'
f.makeViz: no visible global function definition for 'pdf'
f.makeViz: no visible global function definition for 'par'
f.makeViz: no visible global function definition for 'barplot'
f.makeViz: no visible global function definition for 'dev.off'
f.readConfig: no visible global function definition for 'read.table'
f.readData: no visible global function definition for 'read.table'
f.readData: no visible binding for global variable 'IID'
f.readData: no visible binding for global variable 'FID'
f.readData: no visible binding for global variable 'AFF'
f.readData: no visible binding for global variable 'SID'
f.readData: no visible binding for global variable 'gs_all.ls'
f.readData: no visible binding for global variable 'gsid2name.chv'
f.readData: no visible global function definition for 'GRanges'
f.readData: no visible global function definition for 'Rle'
f.readData: no visible global function definition for 'IRanges'
f.readData: no visible global function definition for 'strand'
f.readData: no visible global function definition for 'start'
f.readData: no visible global function definition for 'ranges'
f.readData: no visible global function definition for 'end'
f.readData: no visible global function definition for 'mcols'
f.readData: no visible binding for global variable 'OlpKL_CNV'
f.readData: no visible global function definition for 'stack'
f.readData: no visible binding for global variable 'geneID_type'
f.readData: no visible binding for global variable 'CnvKey'
f.readData: no visible binding for global variable 'OlpKL_SID'
f.readData: no visible binding for global variable 'geneID_TYPE'
f.readData: no visible binding for global variable 'SubjCnvKey'
f.readData: no visible binding for global variable 'GsKey'
f.readData: no visible binding for global variable 'GsID'
f.readData: no visible binding for global variable 'GsName'
f.readData: no visible global function definition for 'cSplit'
f.readData: no visible binding for global variable 'Symbol'
f.readData: no visible global function definition for 'aggregate'
Undefined global functions or variables:
%dopar% AFF BP1 BP2 CHR CnvKey Condition FID GRanges GsID GsKey
GsName IID IRanges OlpKL_CNV OlpKL_SID Rle SID SubjCnvKey Symbol
Symbol_TYPE TYPE aggregate anova as.formula barplot binomial cSplit
detectCores dev.off end foreach geneID geneID_TYPE geneID_type glm
gs_all.ls gsid2name.chv i logit mcols p.adjust par pdf ranges
read.table registerDoParallel stack start strand write.table
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("graphics", "barplot", "par")
importFrom("stats", "aggregate", "anova", "as.formula", "binomial",
"end", "glm", "p.adjust", "start")
importFrom("utils", "read.table", "stack", "write.table")
to your NAMESPACE file.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.4-bioc/meat/cnvGSA.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'cnvGSA' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'cnvGSA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cnvGSA' as cnvGSA_1.18.0.zip
* DONE (cnvGSA)