Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:09 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the lfa package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/lfa.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 984/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
lfa 1.22.0 (landing page) Wei Hao
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: lfa |
Version: 1.22.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:lfa.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings lfa_1.22.0.tar.gz |
StartedAt: 2021-10-15 01:07:14 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 01:09:42 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 147.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: lfa.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:lfa.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings lfa_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/lfa.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 'lfa/DESCRIPTION' ... OK * this is package 'lfa' version '1.22.0' * 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 'lfa' 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 compute.nulls: no visible global function definition for 'rbinom' lfa: no visible global function definition for 'complete.cases' lfa: no visible global function definition for 'residuals' lfa: no visible global function definition for 'lm' lreg: no visible global function definition for 'glm' read.bed: no visible global function definition for 'read.table' trunc.svd: no visible global function definition for 'rnorm' Undefined global functions or variables: complete.cases glm lm rbinom read.table residuals rnorm Consider adding importFrom("stats", "complete.cases", "glm", "lm", "rbinom", "residuals", "rnorm") importFrom("utils", "read.table") 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 ... WARNING Codoc mismatches from documentation object 'lfa': lfa Code: function(X, d, adjustments = NULL, override = FALSE, safety = FALSE, ploidy = 2) Docs: function(X, d, adjustments = NULL, override = FALSE, safety = FALSE) Argument names in code not in docs: ploidy * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... 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/lfa/libs/i386/lfa.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/lfa/libs/x64/lfa.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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed model.gof 23.70 0.13 23.82 sHWE 23.11 0.28 23.39 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed model.gof 27.33 0.22 27.55 sHWE 24.63 0.22 24.85 * 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: 1 WARNING, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/lfa.Rcheck/00check.log' for details.
lfa.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/lfa_1.22.0.tar.gz && rm -rf lfa.buildbin-libdir && mkdir lfa.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=lfa.buildbin-libdir lfa_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL lfa_1.22.0.zip && rm lfa_1.22.0.tar.gz lfa_1.22.0.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 201k 100 201k 0 0 888k 0 --:--:-- --:--:-- --:--:-- 893k install for i386 * installing *source* package 'lfa' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fastmat.c -o fastmat.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c lfa-init.c -o lfa-init.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c lfa.c -o lfa.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c lreg.c -o lreg.o C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o lfa.dll tmp.def fastmat.o lfa-init.o lfa.o lreg.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -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/lfa.buildbin-libdir/00LOCK-lfa/00new/lfa/libs/i386 ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'lfa' finding HTML links ... done af html af_snp html center html centerscale html hgdp_subset html lfa html model.gof html pca_af html read.bed html read.tped.recode html sHWE html trunc.svd 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 'lfa' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fastmat.c -o fastmat.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c lfa-init.c -o lfa-init.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c lfa.c -o lfa.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c lreg.c -o lreg.o C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o lfa.dll tmp.def fastmat.o lfa-init.o lfa.o lreg.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -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/lfa.buildbin-libdir/lfa/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'lfa' as lfa_1.22.0.zip * DONE (lfa) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'lfa' successfully unpacked and MD5 sums checked
lfa.Rcheck/examples_i386/lfa-Ex.timings
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lfa.Rcheck/examples_x64/lfa-Ex.timings
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