William T. Barry
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/safe |
| Branch: RELEASE_3_7 |
| Last Commit: bd236e0 |
| Last Changed Date: 2018-04-30 10:35:01 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:32:24 -0400 (Wed, 17 Oct 2018).
| Package 1306/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| safe 3.20.0 William T. Barry
| 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: safe |
| Version: 3.20.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:safe.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings safe_3.20.0.tar.gz |
| StartedAt: 2018-10-17 04:39:02 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 04:40:44 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 102.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: safe.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:safe.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings safe_3.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/safe.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 'safe/DESCRIPTION' ... OK
* this is package 'safe' version '3.20.0'
* 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 'safe' 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
'library' or 'require' call to 'SparseM' which was already attached by Depends.
Please remove these calls from your code.
'library' or 'require' calls in package code:
'GO.db' 'GOstats' 'PFAM.db' 'Rgraphviz' 'doRNG' 'foreach'
'reactome.db' 'survival'
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
getCOXresiduals: no visible global function definition for 'Surv'
getCOXresiduals: no visible global function definition for 'coxph'
getCOXresiduals: no visible global function definition for 'residuals'
getCmatrix: no visible binding for global variable 'GOTERM'
safe: no visible binding for global variable 'reactomeEXTID2PATHID'
safe: no visible global function definition for 'safe.express'
safe: no visible global function definition for 'getDoParWorkers'
safe: no visible global function definition for '%dorng%'
safe: no visible global function definition for 'foreach'
safe.toptable: no visible binding for global variable 'GOTERM'
safe.toptable: no visible binding for global variable 'PFAMSCOP'
safe.toptable: no visible binding for global variable 'reactome.db'
safedag: no visible binding for global variable 'GOTERM'
safedag: no visible global function definition for 'GOGraph'
safedag: no visible global function definition for 'makeNodeAttrs'
safedag: no visible global function definition for 'subGraph'
safedag: no visible global function definition for 'agopen'
safeplot: no visible binding for global variable 'GOTERM'
safeplot: no visible binding for global variable 'PFAMID'
Undefined global functions or variables:
%dorng% GOGraph GOTERM PFAMID PFAMSCOP Surv agopen coxph foreach
getDoParWorkers makeNodeAttrs reactome.db reactomeEXTID2PATHID
residuals safe.express subGraph
Consider adding
importFrom("stats", "residuals")
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 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
** 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-3.7-bioc/meat/safe.Rcheck/00check.log'
for details.
safe.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/safe_3.20.0.tar.gz && rm -rf safe.buildbin-libdir && mkdir safe.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=safe.buildbin-libdir safe_3.20.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL safe_3.20.0.zip && rm safe_3.20.0.tar.gz safe_3.20.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 164k 100 164k 0 0 2486k 0 --:--:-- --:--:-- --:--:-- 2791k
install for i386
* installing *source* package 'safe' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'safe'
finding HTML links ... done
SAFE-class html
gene.results html
getCmatrix html
p53.stat html
safe-internal html
safe-package html
safe html
safe.toptable html
safedag html
safeplot html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'safe' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'safe' as safe_3.20.0.zip
* DONE (safe)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'safe' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
safe.Rcheck/examples_i386/safe-Ex.timings
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safe.Rcheck/examples_x64/safe-Ex.timings
|