Bioconductor Package Maintainer
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/zlibbioc |
| Branch: RELEASE_3_10 |
| Last Commit: 2e5b107 |
| Last Changed Date: 2019-10-29 13:08:20 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:19:55 -0400 (Wed, 15 Apr 2020).
| Package 1823/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| zlibbioc 1.32.0 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| 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: zlibbioc |
| Version: 1.32.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:zlibbioc.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings zlibbioc_1.32.0.tar.gz |
| StartedAt: 2020-04-15 07:30:38 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 07:31:03 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 25.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: zlibbioc.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:zlibbioc.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings zlibbioc_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/zlibbioc.Rcheck' * using R version 3.6.3 (2020-02-29) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'zlibbioc/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'zlibbioc' version '1.32.0' * 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 'zlibbioc' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE License components with restrictions not permitted: Artistic-2.0 + file LICENSE * 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 ... OK * 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 shell scripts ... 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 include directives 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-3.10-bioc/R/library/zlibbioc/libs/i386/zlib1bioc.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/libs/x64/zlib1bioc.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/libs/i386/zlibbioc.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/libs/x64/zlibbioc.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: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/zlibbioc.Rcheck/00check.log' for details.
zlibbioc.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/zlibbioc_1.32.0.tar.gz && rm -rf zlibbioc.buildbin-libdir && mkdir zlibbioc.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=zlibbioc.buildbin-libdir zlibbioc_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL zlibbioc_1.32.0.zip && rm zlibbioc_1.32.0.tar.gz zlibbioc_1.32.0.zip
###
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install for i386
* installing *source* package 'zlibbioc' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
mkdir -p "C:/Users/biocbuild/bbs-3.10-bioc/meat/zlibbioc.buildbin-libdir/00LOCK-zlibbioc/00new/zlibbioc/include" "C:/Users/biocbuild/bbs-3.10-bioc/meat/zlibbioc.buildbin-libdir/00LOCK-zlibbioc/00new/zlibbioc/libs/i386"
make -C zlib-1.2.5 -fwin32/Makefile.gcc libzbioc.a zlib1bioc.dll
make[1]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpu6IV07/R.INSTALL189020591ba3/zlibbioc/src/zlib-1.2.5'
C:/Rtools/mingw_32/bin/gcc -m32 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o adler32.o adler32.c
C:/Rtools/mingw_32/bin/gcc -m32 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o compress.o compress.c
C:/Rtools/mingw_32/bin/gcc -m32 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o crc32.o crc32.c
C:/Rtools/mingw_32/bin/gcc -m32 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o deflate.o deflate.c
C:/Rtools/mingw_32/bin/gcc -m32 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o gzclose.o gzclose.c
C:/Rtools/mingw_32/bin/gcc -m32 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o gzlib.o gzlib.c
C:/Rtools/mingw_32/bin/gcc -m32 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o gzread.o gzread.c
C:/Rtools/mingw_32/bin/gcc -m32 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o gzwrite.o gzwrite.c
C:/Rtools/mingw_32/bin/gcc -m32 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o infback.o infback.c
C:/Rtools/mingw_32/bin/gcc -m32 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o inffast.o inffast.c
C:/Rtools/mingw_32/bin/gcc -m32 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o inflate.o inflate.c
C:/Rtools/mingw_32/bin/gcc -m32 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o inftrees.o inftrees.c
C:/Rtools/mingw_32/bin/gcc -m32 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o trees.o trees.c
C:/Rtools/mingw_32/bin/gcc -m32 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o uncompr.o uncompr.c
C:/Rtools/mingw_32/bin/gcc -m32 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o zutil.o zutil.c
C:/Rtools/mingw_32/bin/ar rcs libzbioc.a adler32.o compress.o crc32.o deflate.o gzclose.o gzlib.o gzread.o gzwrite.o infback.o inffast.o inflate.o inftrees.o trees.o uncompr.o zutil.o
C:/Rtools/mingw_32/bin/windres --define GCC_WINDRES --target=pe-i386 -o zlibrc.o win32/zlib1.rc
C:/Rtools/mingw_32/bin/gcc -m32 -shared -Wl,--out-implib,libzbiocdll.a \
-o zlib1bioc.dll win32/zlib.def adler32.o compress.o crc32.o deflate.o gzclose.o gzlib.o gzread.o gzwrite.o infback.o inffast.o inflate.o inftrees.o trees.o uncompr.o zutil.o zlibrc.o
C:/Rtools/mingw_32/bin/strip zlib1bioc.dll
make[1]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpu6IV07/R.INSTALL189020591ba3/zlibbioc/src/zlib-1.2.5'
cp zlib-1.2.5/libzbioc.a zlib-1.2.5/zlib1bioc.dll \
"C:/Users/biocbuild/bbs-3.10-bioc/meat/zlibbioc.buildbin-libdir/00LOCK-zlibbioc/00new/zlibbioc/libs/i386"
cp zlib-1.2.5/zconf.h zlib-1.2.5/zlib.h "C:/Users/biocbuild/bbs-3.10-bioc/meat/zlibbioc.buildbin-libdir/00LOCK-zlibbioc/00new/zlibbioc/include"
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_zlibbioc.c -o R_init_zlibbioc.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o zlibbioc.dll tmp.def R_init_zlibbioc.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/zlibbioc.buildbin-libdir/00LOCK-zlibbioc/00new/zlibbioc/libs/i386
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'zlibbioc'
finding HTML links ... done
pkgconfig html
zlibbioc-package 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 'zlibbioc' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
mkdir -p "C:/Users/biocbuild/bbs-3.10-bioc/meat/zlibbioc.buildbin-libdir/zlibbioc/include" "C:/Users/biocbuild/bbs-3.10-bioc/meat/zlibbioc.buildbin-libdir/zlibbioc/libs/x64"
make -C zlib-1.2.5 -fwin32/Makefile.gcc libzbioc.a zlib1bioc.dll
make[1]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpSwBEW3/R.INSTALL181c33045a9b/zlibbioc/src/zlib-1.2.5'
C:/Rtools/mingw_64/bin/gcc -m64 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o adler32.o adler32.c
C:/Rtools/mingw_64/bin/gcc -m64 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o compress.o compress.c
C:/Rtools/mingw_64/bin/gcc -m64 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o crc32.o crc32.c
C:/Rtools/mingw_64/bin/gcc -m64 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o deflate.o deflate.c
C:/Rtools/mingw_64/bin/gcc -m64 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o gzclose.o gzclose.c
C:/Rtools/mingw_64/bin/gcc -m64 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o gzlib.o gzlib.c
C:/Rtools/mingw_64/bin/gcc -m64 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o gzread.o gzread.c
C:/Rtools/mingw_64/bin/gcc -m64 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o gzwrite.o gzwrite.c
C:/Rtools/mingw_64/bin/gcc -m64 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o infback.o infback.c
C:/Rtools/mingw_64/bin/gcc -m64 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o inffast.o inffast.c
C:/Rtools/mingw_64/bin/gcc -m64 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o inflate.o inflate.c
C:/Rtools/mingw_64/bin/gcc -m64 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o inftrees.o inftrees.c
C:/Rtools/mingw_64/bin/gcc -m64 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o trees.o trees.c
C:/Rtools/mingw_64/bin/gcc -m64 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o uncompr.o uncompr.c
C:/Rtools/mingw_64/bin/gcc -m64 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o zutil.o zutil.c
C:/Rtools/mingw_64/bin/ar rcs libzbioc.a adler32.o compress.o crc32.o deflate.o gzclose.o gzlib.o gzread.o gzwrite.o infback.o inffast.o inflate.o inftrees.o trees.o uncompr.o zutil.o
C:/Rtools/mingw_64/bin/windres --define GCC_WINDRES --target=pe-x86-64 -o zlibrc.o win32/zlib1.rc
C:/Rtools/mingw_64/bin/gcc -m64 -shared -Wl,--out-implib,libzbiocdll.a \
-o zlib1bioc.dll win32/zlib.def adler32.o compress.o crc32.o deflate.o gzclose.o gzlib.o gzread.o gzwrite.o infback.o inffast.o inflate.o inftrees.o trees.o uncompr.o zutil.o zlibrc.o
C:/Rtools/mingw_64/bin/strip zlib1bioc.dll
make[1]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpSwBEW3/R.INSTALL181c33045a9b/zlibbioc/src/zlib-1.2.5'
cp zlib-1.2.5/libzbioc.a zlib-1.2.5/zlib1bioc.dll \
"C:/Users/biocbuild/bbs-3.10-bioc/meat/zlibbioc.buildbin-libdir/zlibbioc/libs/x64"
cp zlib-1.2.5/zconf.h zlib-1.2.5/zlib.h "C:/Users/biocbuild/bbs-3.10-bioc/meat/zlibbioc.buildbin-libdir/zlibbioc/include"
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_zlibbioc.c -o R_init_zlibbioc.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o zlibbioc.dll tmp.def R_init_zlibbioc.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/zlibbioc.buildbin-libdir/zlibbioc/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'zlibbioc' as zlibbioc_1.32.0.zip
* DONE (zlibbioc)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'zlibbioc' successfully unpacked and MD5 sums checked
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zlibbioc.Rcheck/examples_i386/zlibbioc-Ex.timings
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zlibbioc.Rcheck/examples_x64/zlibbioc-Ex.timings
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