| Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:56:12 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE CALIB PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 220/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Hui Zhao
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | ERROR | OK | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK |
| Package: CALIB |
| Version: 1.54.0 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/CALIB_1.54.0.tar.gz && rm -rf CALIB.buildbin-libdir && mkdir CALIB.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CALIB.buildbin-libdir CALIB_1.54.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL CALIB_1.54.0.zip && rm CALIB_1.54.0.tar.gz CALIB_1.54.0.zip |
| StartedAt: 2020-10-16 17:00:10 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 17:01:21 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 71.4 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/CALIB_1.54.0.tar.gz && rm -rf CALIB.buildbin-libdir && mkdir CALIB.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CALIB.buildbin-libdir CALIB_1.54.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL CALIB_1.54.0.zip && rm CALIB_1.54.0.tar.gz CALIB_1.54.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 1778k 100 1778k 0 0 7820k 0 --:--:-- --:--:-- --:--:-- 8083k
install for i386
* installing *source* package 'CALIB' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Design.cpp -o Design.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Estimation.cpp -o Estimation.o
Estimation.cpp: In function 'SEXPREC* estimation(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NormalizedData.cpp -o NormalizedData.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ParameterofOneArray.cpp -o ParameterofOneArray.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RawDataofOneArray.cpp -o RawDataofOneArray.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SpikeofOneArray.cpp -o SpikeofOneArray.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o CALIB.dll tmp.def Design.o Estimation.o NormalizedData.o ParameterofOneArray.o RawDataofOneArray.o SpikeofOneArray.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/CALIB.buildbin-libdir/00LOCK-CALIB/00new/CALIB/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CALIB'
finding HTML links ... done
ParameterList-class html
RG html
RGList_CALIB-class html
SpikeList-class html
adjustP2 html
calibReadMe html
cbind html
dim html
dimnames html
estimateParameter html
getColClasses html
merge html
normalizeData html
normdata html
parameter html
plotNormalizedData html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8o1o5N/R.INSTALL10b45e8558d2/CALIB/man/plotNormalizedData.Rd:49: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
plotSpikeCI html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8o1o5N/R.INSTALL10b45e8558d2/CALIB/man/plotSpikeCI.Rd:68: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8o1o5N/R.INSTALL10b45e8558d2/CALIB/man/plotSpikeCI.Rd:95: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
plotSpikeHI html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8o1o5N/R.INSTALL10b45e8558d2/CALIB/man/plotSpikeHI.Rd:69: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8o1o5N/R.INSTALL10b45e8558d2/CALIB/man/plotSpikeHI.Rd:91: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
plotSpikeRG html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8o1o5N/R.INSTALL10b45e8558d2/CALIB/man/plotSpikeRG.Rd:90: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
plotSpikeSpotError html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8o1o5N/R.INSTALL10b45e8558d2/CALIB/man/plotSpikeSpotError.Rd:55: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
read.rg html
read.spike html
spike html
subsetting html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'CALIB' is deprecated and will be removed from Bioconductor
version 3.12
** testing if installed package can be loaded from final location
Warning: Package 'CALIB' is deprecated and will be removed from Bioconductor
version 3.12
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'CALIB' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Design.cpp -o Design.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Estimation.cpp -o Estimation.o
Estimation.cpp: In function 'SEXPREC* estimation(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NormalizedData.cpp -o NormalizedData.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ParameterofOneArray.cpp -o ParameterofOneArray.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RawDataofOneArray.cpp -o RawDataofOneArray.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SpikeofOneArray.cpp -o SpikeofOneArray.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o CALIB.dll tmp.def Design.o Estimation.o NormalizedData.o ParameterofOneArray.o RawDataofOneArray.o SpikeofOneArray.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/CALIB.buildbin-libdir/CALIB/libs/x64
** testing if installed package can be loaded
Warning: Package 'CALIB' is deprecated and will be removed from Bioconductor
version 3.12
* MD5 sums
packaged installation of 'CALIB' as CALIB_1.54.0.zip
* DONE (CALIB)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'CALIB' successfully unpacked and MD5 sums checked