Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:59 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the BufferedMatrixMethods package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrixMethods.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 221/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BufferedMatrixMethods 1.56.0 (landing page) Ben Bolstad
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: BufferedMatrixMethods |
Version: 1.56.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BufferedMatrixMethods.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BufferedMatrixMethods_1.56.0.tar.gz |
StartedAt: 2021-10-14 20:29:58 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 20:30:47 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 48.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BufferedMatrixMethods.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BufferedMatrixMethods.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BufferedMatrixMethods_1.56.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BufferedMatrixMethods.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'BufferedMatrixMethods/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'BufferedMatrixMethods' version '1.56.0' * 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 'BufferedMatrixMethods' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... NOTE 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 in package code: 'affy' 'affyio' Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: 'BufferedMatrix' 'methods' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... NOTE Found the following apparent S3 methods exported but not registered: median.polish.summarize See section 'Registering S3 methods' in the 'Writing R Extensions' manual. * checking replacement functions ... OK * checking foreign function calls ... NOTE Foreign function calls to a different package: .Call("ReadHeader", ..., PACKAGE = "affyio") .Call("read_probeintensities", ..., PACKAGE = "affyio") See chapter 'System and foreign language interfaces' in the 'Writing R Extensions' manual. * checking R code for possible problems ... NOTE NB: .First.lib is obsolete and will not be used in R >= 3.0.0 BufferedMatrix.bg.correct.normalize.quantiles: no visible global function definition for 'is' BufferedMatrix.bg.correct.normalize.quantiles: no visible global function definition for 'duplicate' BufferedMatrix.bg.correct.normalize.quantiles : bg.dens: no visible global function definition for 'density' BufferedMatrix.justRMA: no visible global function definition for 'new' BufferedMatrix.justRMA: no visible global function definition for 'pData' BufferedMatrix.justRMA: no visible global function definition for 'read.celfile.header' BufferedMatrix.justRMA: no visible global function definition for 'cleancdfname' BufferedMatrix.justRMA: no visible global function definition for 'pmindex' BufferedMatrix.justRMA: no visible global function definition for 'geneNames' BufferedMatrix.justRMA: no visible global function definition for 'set.buffer.dim' BufferedMatrix.justRMA: no visible global function definition for 'RowMode' BufferedMatrix.justRMA: no visible global function definition for 'notes<-' BufferedMatrix.read.celfiles: no visible global function definition for 'createBufferedMatrix' BufferedMatrix.read.celfiles: no visible global function definition for 'read.celfile' BufferedMatrix.read.celfiles: no visible global function definition for 'AddColumn' BufferedMatrix.read.probematrix: no visible global function definition for 'new' BufferedMatrix.read.probematrix: no visible global function definition for 'cleancdfname' BufferedMatrix.read.probematrix: no visible global function definition for 'getCdfInfo' BufferedMatrix.read.probematrix: no visible global function definition for 'createBufferedMatrix' BufferedMatrix.read.probematrix: no visible global function definition for 'AddColumn' bg.correct.BufferedMatrix: no visible global function definition for 'is' bg.correct.BufferedMatrix: no visible global function definition for 'duplicate' bg.correct.BufferedMatrix : bg.dens: no visible global function definition for 'density' normalize.BufferedMatrix.quantiles: no visible global function definition for 'is' normalize.BufferedMatrix.quantiles: no visible global function definition for 'duplicate' Undefined global functions or variables: AddColumn RowMode cleancdfname createBufferedMatrix density duplicate geneNames getCdfInfo is new notes<- pData pmindex read.celfile read.celfile.header set.buffer.dim Consider adding importFrom("methods", "is", "new") importFrom("stats", "density") 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 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-3.13-bioc/R/library/BufferedMatrixMethods/libs/i386/BufferedMatrixMethods.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BufferedMatrixMethods/libs/x64/BufferedMatrixMethods.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 examples ... NONE * checking PDF version of manual ... OK * DONE Status: 6 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BufferedMatrixMethods.Rcheck/00check.log' for details.
BufferedMatrixMethods.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/BufferedMatrixMethods_1.56.0.tar.gz && rm -rf BufferedMatrixMethods.buildbin-libdir && mkdir BufferedMatrixMethods.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BufferedMatrixMethods.buildbin-libdir BufferedMatrixMethods_1.56.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BufferedMatrixMethods_1.56.0.zip && rm BufferedMatrixMethods_1.56.0.tar.gz BufferedMatrixMethods_1.56.0.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 11101 100 11101 0 0 133k 0 --:--:-- --:--:-- --:--:-- 135k install for i386 * installing *source* package 'BufferedMatrixMethods' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BufferedMatrix/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init_package.c -o init_package.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BufferedMatrix/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c preprocess_bm.c -o preprocess_bm.o preprocess_bm.c: In function 'bm_rma_bg_correct': preprocess_bm.c:344:7: warning: unused variable 'i' [-Wunused-variable] int i,j; ^ preprocess_bm.c: In function 'R_bm_rma_bg_correct': preprocess_bm.c:378:7: warning: unused variable 'current_mode' [-Wunused-variable] int current_mode; ^~~~~~~~~~~~ preprocess_bm.c: In function 'R_bm_quantile_normalize': preprocess_bm.c:593:7: warning: unused variable 'current_mode' [-Wunused-variable] int current_mode; ^~~~~~~~~~~~ preprocess_bm.c: In function 'do_RMA_buffmat': preprocess_bm.c:924:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable] int first_ind; ^~~~~~~~~ preprocess_bm.c: In function 'R_bm_rma_bg_correct_quantile_normalize': preprocess_bm.c:1151:7: warning: unused variable 'current_mode' [-Wunused-variable] int current_mode; ^~~~~~~~~~~~ At top level: preprocess_bm.c:453:12: warning: 'min' defined but not used [-Wunused-function] static int min(int x1,int x2){ ^~~ C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o BufferedMatrixMethods.dll tmp.def init_package.o preprocess_bm.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/BufferedMatrixMethods.buildbin-libdir/00LOCK-BufferedMatrixMethods/00new/BufferedMatrixMethods/libs/i386 ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'BufferedMatrixMethods' finding HTML links ... done BM_affyDataInput html BM_justRMA html BM_readcelfiles html rmapreprocess.bufferedmatrix html ** building package indices ** 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 'BufferedMatrixMethods' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BufferedMatrix/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init_package.c -o init_package.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BufferedMatrix/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c preprocess_bm.c -o preprocess_bm.o preprocess_bm.c: In function 'bm_rma_bg_correct': preprocess_bm.c:344:7: warning: unused variable 'i' [-Wunused-variable] int i,j; ^ preprocess_bm.c: In function 'R_bm_rma_bg_correct': preprocess_bm.c:378:7: warning: unused variable 'current_mode' [-Wunused-variable] int current_mode; ^~~~~~~~~~~~ preprocess_bm.c: In function 'R_bm_quantile_normalize': preprocess_bm.c:593:7: warning: unused variable 'current_mode' [-Wunused-variable] int current_mode; ^~~~~~~~~~~~ preprocess_bm.c: In function 'do_RMA_buffmat': preprocess_bm.c:924:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable] int first_ind; ^~~~~~~~~ preprocess_bm.c: In function 'R_bm_rma_bg_correct_quantile_normalize': preprocess_bm.c:1151:7: warning: unused variable 'current_mode' [-Wunused-variable] int current_mode; ^~~~~~~~~~~~ At top level: preprocess_bm.c:453:12: warning: 'min' defined but not used [-Wunused-function] static int min(int x1,int x2){ ^~~ C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o BufferedMatrixMethods.dll tmp.def init_package.o preprocess_bm.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/BufferedMatrixMethods.buildbin-libdir/BufferedMatrixMethods/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'BufferedMatrixMethods' as BufferedMatrixMethods_1.56.0.zip * DONE (BufferedMatrixMethods) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'BufferedMatrixMethods' successfully unpacked and MD5 sums checked