Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:07:17 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the safe package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/safe.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1686/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
safe 3.34.0 (landing page) Ludwig Geistlinger
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: safe |
Version: 3.34.0 |
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:safe.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings safe_3.34.0.tar.gz |
StartedAt: 2022-04-13 02:12:18 -0400 (Wed, 13 Apr 2022) |
EndedAt: 2022-04-13 02:14:29 -0400 (Wed, 13 Apr 2022) |
EllapsedTime: 131.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: safe.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:safe.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings safe_3.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/safe.Rcheck' * using R version 4.1.3 (2022-03-10) * 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 '3.34.0' * 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-3.14-bioc/meat/safe.Rcheck/00check.log' for details.
safe.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/safe_3.34.0.tar.gz && rm -rf safe.buildbin-libdir && mkdir safe.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=safe.buildbin-libdir safe_3.34.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL safe_3.34.0.zip && rm safe_3.34.0.tar.gz safe_3.34.0.zip ### ############################################################################## ############################################################################## % 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 718k 0 --:--:-- --:--:-- --:--:-- 722k install for i386 * installing *source* package 'safe' ... ** using staged installation ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'safe' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'safe' as safe_3.34.0.zip * DONE (safe) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'safe' successfully unpacked and MD5 sums checked
safe.Rcheck/examples_i386/safe-Ex.timings
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safe.Rcheck/examples_x64/safe-Ex.timings
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