Back to Multiple platform build/check report for BioC 3.8 |
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This page was generated on 2019-04-13 11:24:53 -0400 (Sat, 13 Apr 2019).
Package 1456/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
sincell 1.14.1 Miguel Julia
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | NA | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: sincell |
Version: 1.14.1 |
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sincell.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings sincell_1.14.1.tar.gz |
StartedAt: 2019-04-13 05:35:24 -0400 (Sat, 13 Apr 2019) |
EndedAt: 2019-04-13 05:38:05 -0400 (Sat, 13 Apr 2019) |
EllapsedTime: 161.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sincell.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sincell.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings sincell_1.14.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/sincell.Rcheck' * using R version 3.5.3 (2019-03-11) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'sincell/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'sincell' version '1.14.1' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 'sincell' 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 sc_AssociationOfCellsHierarchyWithAGeneSet: no visible global function definition for 'cor' sc_ComparissonOfGraphs: no visible global function definition for 'cor' sc_ComparissonOfGraphs: no visible global function definition for 'plot' sc_ComparissonOfGraphs: no visible global function definition for 'hclust' sc_DimensionalityReductionObj: no visible global function definition for 'prcomp' sc_DimensionalityReductionObj: no visible global function definition for 'cmdscale' sc_GraphBuilderObj: no visible global function definition for 'combn' sc_InSilicoCellsReplicatesObj: no visible binding for global variable 'var' sc_InSilicoCellsReplicatesObj : f_mclapply: no visible global function definition for 'runif' sc_InSilicoCellsReplicatesObj : expressedvar: no visible global function definition for 'var' sc_InSilicoCellsReplicatesObj : f_mclapply: no visible binding for global variable 'rnorm' sc_InSilicoCellsReplicatesObj: no visible global function definition for 'quantile' sc_InSilicoCellsReplicatesObj : f_mclapply: no visible global function definition for 'rnbinom' sc_InitializingSincellObject: no visible binding for global variable 'var' sc_StatisticalSupportByGeneSubsampling: no visible global function definition for 'cor' sc_StatisticalSupportByReplacementWithInSilicoCellsReplicates: no visible global function definition for 'cor' sc_clusterObj: no visible global function definition for 'hclust' sc_clusterObj: no visible global function definition for 'cutree' sc_distanceObj: no visible global function definition for 'cor' sc_marker2color: no visible global function definition for 'colorRampPalette' Undefined global functions or variables: cmdscale colorRampPalette combn cor cutree hclust plot prcomp quantile rnbinom rnorm runif var Consider adding importFrom("grDevices", "colorRampPalette") importFrom("graphics", "plot") importFrom("stats", "cmdscale", "cor", "cutree", "hclust", "prcomp", "quantile", "rnbinom", "rnorm", "runif", "var") importFrom("utils", "combn") 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-3.8-bioc/R/library/sincell/libs/i386/sincell.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) Found 'rand', possibly from 'rand' (C) Found 'srand', possibly from 'srand' (C) 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 Examples with CPU or elapsed time > 5s user system elapsed sc_StatisticalSupportByGeneSubsampling 16.27 0.02 16.28 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed sc_StatisticalSupportByGeneSubsampling 16.53 0.04 16.57 * 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-3.8-bioc/meat/sincell.Rcheck/00check.log' for details.
sincell.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/sincell_1.14.1.tar.gz && rm -rf sincell.buildbin-libdir && mkdir sincell.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sincell.buildbin-libdir sincell_1.14.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL sincell_1.14.1.zip && rm sincell_1.14.1.tar.gz sincell_1.14.1.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 543k 100 543k 0 0 12.7M 0 --:--:-- --:--:-- --:--:-- 13.9M install for i386 * installing *source* package 'sincell' ... ** libs C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pseudoreplicatesbymodel.cpp -o pseudoreplicatesbymodel.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pseudoreplicatesbynoise.cpp -o pseudoreplicatesbynoise.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pseudoreplicatesbynoise_cv2.cpp -o pseudoreplicatesbynoise_cv2.o C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c sstalgorithm.cpp -o sstalgorithm.o sstalgorithm.cpp: In function 'Rcpp::NumericVector sstalgorithm(Rcpp::NumericVector, int, Rcpp::NumericMatrix)': sstalgorithm.cpp:28:17: warning: 'disty' may be used uninitialized in this function [-Wmaybe-uninitialized] out[2] = disty; ^ sstalgorithm.cpp:27:17: warning: 'distx' may be used uninitialized in this function [-Wmaybe-uninitialized] out[1] = distx; ^ C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o sincell.dll tmp.def RcppExports.o pseudoreplicatesbymodel.o pseudoreplicatesbynoise.o pseudoreplicatesbynoise_cv2.o sstalgorithm.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/sincell.buildbin-libdir/sincell/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'sincell' finding HTML links ... done ExpressionMatrix html f_distance2vector html geneset.list html knnalgorithm html pseudoreplicatesbymodel html pseudoreplicatesbynoise html pseudoreplicatesbynoise_cv2 html sc_AssociationOfCellsHierarchyWithAGeneSet html sc_ComparissonOfGraphs html sc_DimensionalityReductionObj html sc_GraphBuilderObj html sc_InSilicoCellsReplicatesObj html sc_InitializingSincellObject html sc_StatisticalSupportByGeneSubsampling html sc_StatisticalSupportByReplacementWithInSilicoCellsReplicates html sc_clusterObj html sc_distanceObj html sc_marker2color html sstalgorithm html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'sincell' ... ** libs C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pseudoreplicatesbymodel.cpp -o pseudoreplicatesbymodel.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pseudoreplicatesbynoise.cpp -o pseudoreplicatesbynoise.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pseudoreplicatesbynoise_cv2.cpp -o pseudoreplicatesbynoise_cv2.o C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c sstalgorithm.cpp -o sstalgorithm.o sstalgorithm.cpp: In function 'Rcpp::NumericVector sstalgorithm(Rcpp::NumericVector, int, Rcpp::NumericMatrix)': sstalgorithm.cpp:28:17: warning: 'disty' may be used uninitialized in this function [-Wmaybe-uninitialized] out[2] = disty; ^ sstalgorithm.cpp:27:17: warning: 'distx' may be used uninitialized in this function [-Wmaybe-uninitialized] out[1] = distx; ^ C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o sincell.dll tmp.def RcppExports.o pseudoreplicatesbymodel.o pseudoreplicatesbynoise.o pseudoreplicatesbynoise_cv2.o sstalgorithm.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/sincell.buildbin-libdir/sincell/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'sincell' as sincell_1.14.1.zip * DONE (sincell) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library' package 'sincell' successfully unpacked and MD5 sums checked In R CMD INSTALL
sincell.Rcheck/examples_i386/sincell-Ex.timings
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sincell.Rcheck/examples_x64/sincell-Ex.timings
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