iGC 1.1.0
Liang-Bo Wang
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/iGC | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### rm -rf iGC.buildbin-libdir iGC.Rcheck && mkdir iGC.buildbin-libdir iGC.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=iGC.buildbin-libdir iGC_1.1.0.tar.gz >iGC.Rcheck\00install.out 2>&1 && cp iGC.Rcheck\00install.out iGC-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=iGC.buildbin-libdir --install="check:iGC-install.out" --force-multiarch --no-vignettes --timings iGC_1.1.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/iGC.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'iGC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iGC' version '1.1.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doMC'
* 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 'iGC' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.5Mb
sub-directories of 1Mb or more:
extdata 5.6Mb
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
create_gene_cna: no visible binding for global variable 'hg19DBNM'
create_gene_cna: no visible binding for global variable 'Gene.Symbol'
create_gene_cna: no visible binding for global variable 'GENE'
direct_gene_cna : <anonymous>: no visible binding for global variable
'GENE'
direct_gene_cna : <anonymous>: no visible binding for global variable
'gain_loss'
direct_gene_cna: no visible binding for global variable 'GENE'
find_cna_driven_gene: no visible binding for global variable 'GENE'
find_cna_driven_gene : exp_grouptest_driven_by_cna: no visible binding
for global variable 'Gain'
find_cna_driven_gene : exp_grouptest_driven_by_cna: no visible binding
for global variable 'GENE'
find_cna_driven_gene : exp_grouptest_driven_by_cna: no visible binding
for global variable 'Loss'
find_cna_driven_gene: no visible binding for global variable 'p_value'
find_cna_driven_gene: no visible binding for global variable 'fdr'
find_cna_driven_gene: no visible binding for global variable
'vs_rest_exp_diff'
process_cna_per_sample: no visible binding for global variable
'gain_loss'
process_cna_per_sample: no visible binding for global variable
'Segment_Mean'
process_cna_per_sample: no visible binding for global variable
'Chromosome'
process_cna_per_sample: no visible binding for global variable 'Start'
process_cna_per_sample: no visible binding for global variable 'End'
process_cna_per_sample: no visible binding for global variable
'Gene.Symbol'
process_cna_per_sample: no visible binding for global variable
'cur_sample'
process_cna_per_sample_direct: no visible binding for global variable
'Segment_Mean'
process_cna_per_sample_direct: no visible binding for global variable
'gain_loss'
process_cna_per_sample_direct: no visible binding for global variable
'cna_val'
read_cna_geo: no visible binding for global variable 'GENE'
read_cna_geo: no visible binding for global variable 'Segment_Mean'
Undefined global functions or variables:
Chromosome End GENE Gain Gene.Symbol Loss Segment_Mean Start cna_val
cur_sample fdr gain_loss hg19DBNM p_value vs_rest_exp_diff
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [2s] OK
** running examples for arch 'x64' ... [2s] 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: 3 NOTEs
See
'c:/biocbld/bbs-3.3-bioc/meat/iGC.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'iGC' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'iGC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iGC' as iGC_1.1.0.zip
* DONE (iGC)