Back to Multiple platform build/check report for BioC 3.10 |
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This page was generated on 2020-04-15 12:17:59 -0400 (Wed, 15 Apr 2020).
Package 215/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
CALIB 1.52.0 Hui Zhao
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: CALIB |
Version: 1.52.0 |
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CALIB.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings CALIB_1.52.0.tar.gz |
StartedAt: 2020-04-15 01:45:48 -0400 (Wed, 15 Apr 2020) |
EndedAt: 2020-04-15 01:47:00 -0400 (Wed, 15 Apr 2020) |
EllapsedTime: 72.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CALIB.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CALIB.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings CALIB_1.52.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/CALIB.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 'CALIB/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'CALIB' version '1.52.0' * 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 'CALIB' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: 'limma' 'methods' A package should be listed in only one of these fields. * 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 ... NOTE Found the following apparent S3 methods exported but not registered: [.ParameterList [.RGList_CALIB [.SpikeList cbind.ParameterList cbind.RGList_CALIB cbind.SpikeList dim.RGList_CALIB dim.SpikeList dimnames.RGList_CALIB dimnames.SpikeList length.RGList_CALIB length.SpikeList merge.RGList_CALIB merge.SpikeList rbind.RGList_CALIB rbind.SpikeList See section 'Registering S3 methods' in the 'Writing R Extensions' manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE read.rg: warning in scan(fullname, what = "", sep = sep, quote = quote, skip = 1, nlines = 1, quiet = TRUE, allowEscape = FALSE): partial argument match of 'allowEscape' to 'allowEscapes' getColClasses: no visible global function definition for 'namesInFun' plotSpikeCI: no visible binding for global variable 'otherindex' read.rg: no visible global function definition for 'readBlueFuseHeader' read.spike: no visible binding for global variable 'files' Undefined global functions or variables: files namesInFun otherindex readBlueFuseHeader * 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-3.10-bioc/R/library/CALIB/libs/i386/CALIB.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/CALIB/libs/x64/CALIB.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (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 estimateParameter 8.57 0 8.56 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed estimateParameter 8.79 0.03 9.01 * 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: 4 NOTEs See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/CALIB.Rcheck/00check.log' for details.
CALIB.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/CALIB_1.52.0.tar.gz && rm -rf CALIB.buildbin-libdir && mkdir CALIB.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CALIB.buildbin-libdir CALIB_1.52.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL CALIB_1.52.0.zip && rm CALIB_1.52.0.tar.gz CALIB_1.52.0.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 1773k 100 1773k 0 0 34.9M 0 --:--:-- --:--:-- --:--:-- 37.6M install for i386 * installing *source* package 'CALIB' ... ** using staged installation ** libs C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c Design.cpp -o Design.o C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"}; ^ Estimation.cpp:147:78: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] Estimation.cpp:147:78: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] Estimation.cpp:147:78: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] Estimation.cpp:147:78: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] Estimation.cpp:147:78: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] Estimation.cpp:147:78: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] Estimation.cpp:147:78: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c NormalizedData.cpp -o NormalizedData.o C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c ParameterofOneArray.cpp -o ParameterofOneArray.o C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c RawDataofOneArray.cpp -o RawDataofOneArray.o C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c SpikeofOneArray.cpp -o SpikeofOneArray.o C:/Rtools/mingw_32/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-3~1.10-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.10-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 plotSpikeCI html plotSpikeHI html plotSpikeRG html plotSpikeSpotError html 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 ** 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 'CALIB' ... ** libs C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c Design.cpp -o Design.o C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"}; ^ Estimation.cpp:147:78: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] Estimation.cpp:147:78: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] Estimation.cpp:147:78: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] Estimation.cpp:147:78: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] Estimation.cpp:147:78: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] Estimation.cpp:147:78: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] Estimation.cpp:147:78: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c NormalizedData.cpp -o NormalizedData.o C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c ParameterofOneArray.cpp -o ParameterofOneArray.o C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c RawDataofOneArray.cpp -o RawDataofOneArray.o C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c SpikeofOneArray.cpp -o SpikeofOneArray.o C:/Rtools/mingw_64/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-3~1.10-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/CALIB.buildbin-libdir/CALIB/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'CALIB' as CALIB_1.52.0.zip * DONE (CALIB) * installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library' package 'CALIB' successfully unpacked and MD5 sums checked
CALIB.Rcheck/examples_i386/CALIB-Ex.timings
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CALIB.Rcheck/examples_x64/CALIB-Ex.timings
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