CINdex 1.4.0
Yuriy Gusev
| Snapshot Date: 2017-08-14 17:17:40 -0400 (Mon, 14 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/CINdex | | Last Changed Rev: 129126 / Revision: 131921 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf CINdex.buildbin-libdir CINdex.Rcheck && mkdir CINdex.buildbin-libdir CINdex.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CINdex.buildbin-libdir CINdex_1.4.0.tar.gz >CINdex.Rcheck\00install.out 2>&1 && cp CINdex.Rcheck\00install.out CINdex-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=CINdex.buildbin-libdir --install="check:CINdex-install.out" --force-multiarch --no-vignettes --timings CINdex_1.4.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/CINdex.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CINdex/DESCRIPTION' ... OK
* this is package 'CINdex' version '1.4.0'
* 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 ... NOTE
Found the following non-portable file paths:
CINdex/vignettes/output_cyto_plots/2.25_1.75_unnormalized_sum/chr_10_dataMatrix_2.25_1.75_unnormalized_sum.png
CINdex/vignettes/output_cyto_plots/2.25_1.75_unnormalized_sum/chr_11_dataMatrix_2.25_1.75_unnormalized_sum.png
CINdex/vignettes/output_cyto_plots/2.25_1.75_unnormalized_sum/chr_12_dataMatrix_2.25_1.75_unnormalized_sum.png
CINdex/vignettes/output_cyto_plots/2.25_1.75_unnormalized_sum/chr_13_dataMatrix_2.25_1.75_unnormalized_sum.png
CINdex/vignettes/output_cyto_plots/2.25_1.75_unnormalized_sum/chr_14_dataMatrix_2.25_1.75_unnormalized_sum.png
CINdex/vignettes/output_cyto_plots/2.25_1.75_unnormalized_sum/chr_15_dataMatrix_2.25_1.75_unnormalized_sum.png
CINdex/vignettes/output_cyto_plots/2.25_1.75_unnormalized_sum/chr_16_dataMatrix_2.25_1.75_unnormalized_sum.png
CINdex/vignettes/output_cyto_plots/2.25_1.75_unnormalized_sum/chr_17_dataMatrix_2.25_1.75_unnormalized_sum.png
CINdex/vignettes/output_cyto_plots/2.25_1.75_unnormalized_sum/chr_18_dataMatrix_2.25_1.75_unnormalized_sum.png
CINdex/vignettes/output_cyto_plots/2.25_1.75_unnormalized_sum/chr_19_dataMatrix_2.25_1.75_unnormalized_sum.png
CINdex/vignettes/output_cyto_plots/2.25_1.75_unnormalized_sum/chr_1_dataMatrix_2.25_1.75_unnormalized_sum.png
CINdex/vignettes/output_cyto_plots/2.25_1.75_unnormalized_sum/chr_20_dataMatrix_2.25_1.75_unnormalized_sum.png
CINdex/vignettes/output_cyto_plots/2.25_1.75_unnormalized_sum/chr_21_dataMatrix_2.25_1.75_unnormalized_sum.png
CINdex/vignettes/output_cyto_plots/2.25_1.75_unnormalized_sum/chr_22_dataMatrix_2.25_1.75_unnormalized_sum.png
CINdex/vignettes/output_cyto_plots/2.25_1.75_unnormalized_sum/chr_2_dataMatrix_2.25_1.75_unnormalized_sum.png
CINdex/vignettes/output_cyto_plots/2.25_1.75_unnormalized_sum/chr_3_dataMatrix_2.25_1.75_unnormalized_sum.png
CINdex/vignettes/output_cyto_plots/2.25_1.75_unnormalized_sum/chr_4_dataMatrix_2.25_1.75_unnormalized_sum.png
CINdex/vignettes/output_cyto_plots/2.25_1.75_unnormalized_sum/chr_5_dataMatrix_2.25_1.75_unnormalized_sum.png
CINdex/vignettes/output_cyto_plots/2.25_1.75_unnormalized_sum/chr_6_dataMatrix_2.25_1.75_unnormalized_sum.png
CINdex/vignettes/output_cyto_plots/2.25_1.75_unnormalized_sum/chr_7_dataMatrix_2.25_1.75_unnormalized_sum.png
CINdex/vignettes/output_cyto_plots/2.25_1.75_unnormalized_sum/chr_8_dataMatrix_2.25_1.75_unnormalized_sum.png
CINdex/vignettes/output_cyto_plots/2.25_1.75_unnormalized_sum/chr_9_dataMatrix_2.25_1.75_unnormalized_sum.png
Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'CINdex' can be installed ... OK
* checking installed package size ... NOTE
installed size is 18.4Mb
sub-directories of 1Mb or more:
data 17.7Mb
* 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
comp.heatmap: no visible binding for global variable 'dataMatrix'
process.probe.anno: no visible binding for global variable 'ID'
process.probe.anno: no visible binding for global variable 'midpoint'
process.reference.genome: no visible binding for global variable
'chrom'
process.reference.genome: no visible binding for global variable 'name'
process.reference.genome: no visible binding for global variable
'stain'
Undefined global functions or variables:
ID chrom dataMatrix midpoint name stain
* 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' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
run.cin.cyto 14.43 0.51 14.97
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
run.cin.cyto 16.94 0.67 17.61
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'RunTests.R'
OK
** running tests for arch 'x64' ...
Running 'RunTests.R'
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:/Users/biocbuild/bbs-3.5-bioc/meat/CINdex.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'CINdex' ...
** 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 'CINdex' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CINdex' as CINdex_1.4.0.zip
* DONE (CINdex)