Andrew J. Bass
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/subSeq |
| Branch: RELEASE_3_7 |
| Last Commit: 4014bea |
| Last Changed Date: 2018-04-30 10:35:39 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:41:19 -0400 (Wed, 17 Oct 2018).
| Package 1444/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| subSeq 1.10.0 Andrew J. Bass
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: subSeq |
| Version: 1.10.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:subSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings subSeq_1.10.0.tar.gz |
| StartedAt: 2018-10-17 05:05:31 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 05:10:02 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 271.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: subSeq.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:subSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings subSeq_1.10.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/subSeq.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'subSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'subSeq' version '1.10.0'
* 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 'subSeq' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DESeq2: no visible global function definition for 'selectMethod'
ccc: no visible global function definition for 'cov'
ccc: no visible global function definition for 'var'
generateSubsampledMatrix : <anonymous>: no visible global function
definition for 'rbinom'
plot.subsamples: no visible global function definition for 'plot'
plot.summary.subsamples: no visible binding for global variable
'metric'
plot.summary.subsamples: no visible binding for global variable 'value'
plot.summary.subsamples: no visible binding for global variable
'significant'
plot.summary.subsamples: no visible binding for global variable
'percent'
plot.summary.subsamples: no visible binding for global variable
'method'
plot.summary.subsamples: no visible binding for global variable 'depth'
plot.summary.subsamples: no visible binding for global variable
'average.depth'
plot.summary.subsamples: no visible binding for global variable
'average.value'
subsample: no visible binding for global variable 'proportion'
subsample: no visible binding for global variable 'replication'
subsample: no visible binding for global variable '.'
subsample: no visible binding for global variable 'pvalue'
summary.subsamples: no visible binding for global variable 'count'
summary.subsamples: no visible binding for global variable 'method'
summary.subsamples: no visible binding for global variable 'depth'
summary.subsamples: no visible binding for global variable 'pvalue'
summary.subsamples: no visible binding for global variable 'proportion'
summary.subsamples: no visible binding for global variable
'replication'
summary.subsamples: no visible global function definition for
'p.adjust'
summary.subsamples: no visible binding for global variable 'ID'
summary.subsamples: no visible binding for global variable 'padj'
summary.subsamples: no visible binding for global variable
'coefficient'
summary.subsamples: no visible binding for global variable
'o.coefficient'
summary.subsamples: no visible global function definition for 'cor'
summary.subsamples: no visible binding for global variable 'valid'
summary.subsamples: no visible binding for global variable 'o.lfdr'
summary.subsamples: no visible binding for global variable 'o.padj'
summary.subsamples: no visible binding for global variable
'significant'
summary.subsamples: no visible binding for global variable 'estFDP'
summary.subsamples: no visible binding for global variable 'rFDP'
summary.subsamples: no visible binding for global variable 'metric'
summary.subsamples: no visible binding for global variable 'value'
summary.subsamples: no visible binding for global variable 'percent'
voomLimma: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
. ID average.depth average.value coefficient cor count cov depth
estFDP method metric model.matrix o.coefficient o.lfdr o.padj
p.adjust padj percent plot proportion pvalue rFDP rbinom replication
selectMethod significant valid value var
Consider adding
importFrom("graphics", "plot")
importFrom("methods", "selectMethod")
importFrom("stats", "cor", "cov", "model.matrix", "p.adjust", "rbinom",
"var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
generateSubsampledMatrix 36.09 0.88 37.07
getSeed 31.44 0.10 31.55
subsample 27.77 0.09 27.86
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
generateSubsampledMatrix 39.63 0.42 40.05
getSeed 35.92 0.06 35.99
subsample 30.23 0.03 30.29
* 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 NOTE
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/subSeq.Rcheck/00check.log'
for details.
subSeq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/subSeq_1.10.0.tar.gz && rm -rf subSeq.buildbin-libdir && mkdir subSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=subSeq.buildbin-libdir subSeq_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL subSeq_1.10.0.zip && rm subSeq_1.10.0.tar.gz subSeq_1.10.0.zip
###
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install for i386
* installing *source* package 'subSeq' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'subSeq'
finding HTML links ... done
combineSubsamples html
generateSubsampledMatrix html
getSeed html
hammer html
plot.subsamples html
plot.summary.subsamples html
ss html
subsample html
summary.subsamples html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'subSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'subSeq' as subSeq_1.10.0.zip
* DONE (subSeq)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'subSeq' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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subSeq.Rcheck/examples_i386/subSeq-Ex.timings
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subSeq.Rcheck/examples_x64/subSeq-Ex.timings
|