Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:34:18 -0400 (Wed, 17 Oct 2018).
Package 277/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
CNTools 1.36.0 J. Zhang
| 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: CNTools |
Version: 1.36.0 |
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CNTools_1.36.0.tar.gz |
StartedAt: 2018-10-17 01:13:59 -0400 (Wed, 17 Oct 2018) |
EndedAt: 2018-10-17 01:16:23 -0400 (Wed, 17 Oct 2018) |
EllapsedTime: 144.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CNTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CNTools_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/CNTools.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 'CNTools/DESCRIPTION' ... OK * this is package 'CNTools' version '1.36.0' * 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 'CNTools' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. Malformed Description field: should contain one or more complete sentences. * 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' calls to packages already attached by Depends: 'methods' 'tools' Please remove these calls from your code. Packages in Depends field not imported from: 'methods' 'tools' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. ':::' call which should be '::': 'genefilter:::genefilter' See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: 'getCommonSegValues' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File 'CNTools/R/zzz.R': .onLoad calls: require("methods", quietly = TRUE) require("tools", quietly = TRUE) Package startup functions should not change the search path. See section 'Good practice' in '?.onAttach'. filterByMad: no visible binding for global variable 'mad' filterByMad: no visible global function definition for 'quantile' getPairCor : pair2Cor: no visible global function definition for 'cor' getPairDist : pair2Dist: no visible global function definition for 'dist' getPairDist: no visible global function definition for 'as.dist' getCor,RS: no visible global function definition for 'cor' getDist,RS: no visible global function definition for 'dist' Undefined global functions or variables: as.dist cor dist mad quantile Consider adding importFrom("stats", "as.dist", "cor", "dist", "mad", "quantile") 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/CNTools/libs/i386/CNTools.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * 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: 4 NOTEs See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/CNTools.Rcheck/00check.log' for details.
CNTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/CNTools_1.36.0.tar.gz && rm -rf CNTools.buildbin-libdir && mkdir CNTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNTools.buildbin-libdir CNTools_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL CNTools_1.36.0.zip && rm CNTools_1.36.0.tar.gz CNTools_1.36.0.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 775k 100 775k 0 0 11.3M 0 --:--:-- --:--:-- --:--:-- 12.6M install for i386 * installing *source* package 'CNTools' ... ** libs C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c getratios.c -o getratios.o C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o CNTools.dll tmp.def getratios.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/CNTools.buildbin-libdir/CNTools/libs/i386 ** R ** data ** byte-compile and prepare package for lazy loading Creating a new generic function for 'start' in package 'CNTools' Creating a new generic function for 'end' in package 'CNTools' Creating a generic function for 'genefilter' from package 'genefilter' in package 'CNTools' ** help *** installing help indices converting help for package 'CNTools' finding HTML links ... done CNSeg-class html RS-class html cor-methods html diffBy-methods html dist-methods html genefilter-methods html getRS-methods html madFilter-methods html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'CNTools' ... ** libs C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c getratios.c -o getratios.o C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o CNTools.dll tmp.def getratios.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/CNTools.buildbin-libdir/CNTools/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'CNTools' as CNTools_1.36.0.zip * DONE (CNTools) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library' package 'CNTools' successfully unpacked and MD5 sums checked In R CMD INSTALL
CNTools.Rcheck/examples_i386/CNTools-Ex.timings
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CNTools.Rcheck/examples_x64/CNTools-Ex.timings
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