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BioC 2.13: CHECK report for CGEN on moscato1

This page was generated on 2014-04-05 09:50:07 -0700 (Sat, 05 Apr 2014).

Package 119/750HostnameOS / ArchBUILDCHECKBUILD BIN
CGEN 2.4.0
William Wheeler
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/CGEN
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: CGEN
Version: 2.4.0
Command: rm -rf CGEN.buildbin-libdir && mkdir CGEN.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CGEN.buildbin-libdir CGEN_2.4.0.tar.gz >CGEN-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=CGEN.buildbin-libdir --install="check:CGEN-install.out" --force-multiarch --no-vignettes --timings CGEN_2.4.0.tar.gz && mv CGEN.buildbin-libdir/* CGEN.Rcheck/ && rmdir CGEN.buildbin-libdir
StartedAt: 2014-04-05 02:51:07 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:54:15 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 188.1 seconds
RetCode: 0
Status:  OK  
CheckDir: CGEN.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/CGEN.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CGEN/DESCRIPTION' ... OK
* this is package 'CGEN' version '2.4.0'
* 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 'CGEN' 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:
  GPL-2 + 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 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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 'D:/biocbld/bbs-2.13-bioc/meat/CGEN.buildbin-libdir/CGEN/libs/i386/CGEN.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-2.13-bioc/meat/CGEN.buildbin-libdir/CGEN/libs/x64/CGEN.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.  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 installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'vignette.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [54s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
getMatchedSets 27.46   0.23   27.69
snp.matched    23.21   0.00   23.21
** running examples for arch 'x64' ... [53s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
getMatchedSets 28.42   0.14   28.56
snp.matched    20.56   0.00   20.56
* 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/CGEN.Rcheck/00check.log'
for details.

CGEN.Rcheck/00install.out:


install for i386

* installing *source* package 'CGEN' ...
** libs
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Additive.c -o Additive.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c CML.c -o CML.o
CML.c:1198:13: warning: 'print_dVec' defined but not used [-Wunused-function]
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ccl.c -o ccl.o
ccl.c: In function 'ccl_optim':
ccl.c:78:2: warning: passing argument 1 of 'Rf_error' makes pointer from integer without a cast [enabled by default]
D:/biocbld/BBS-2˜1.13-/R/include/R_ext/Error.h:33:6: note: expected 'const char *' but argument is of type 'int'
ccl.c: In function 'factorial':
ccl.c:478:2: warning: passing argument 1 of 'Rf_error' makes pointer from integer without a cast [enabled by default]
D:/biocbld/BBS-2˜1.13-/R/include/R_ext/Error.h:33:6: note: expected 'const char *' but argument is of type 'int'
ccl.c: At top level:
ccl.c:386:13: warning: 'tree_print' defined but not used [-Wunused-function]
gfortran -m32     -O3  -mtune=core2 -c csclust.f -o csclust.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c fsclust.c -o fsclust.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c hcl.c -o hcl.o
hcl.c: In function 'hcl_optim':
hcl.c:72:2: warning: passing argument 1 of 'Rf_error' makes pointer from integer without a cast [enabled by default]
D:/biocbld/BBS-2˜1.13-/R/include/R_ext/Error.h:33:6: note: expected 'const char *' but argument is of type 'int'
hcl.c: In function 'factorial':
hcl.c:467:2: warning: passing argument 1 of 'Rf_error' makes pointer from integer without a cast [enabled by default]
D:/biocbld/BBS-2˜1.13-/R/include/R_ext/Error.h:33:6: note: expected 'const char *' but argument is of type 'int'
hcl.c: At top level:
hcl.c:375:13: warning: 'tree_print' defined but not used [-Wunused-function]
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c pmatch.c -o pmatch.o
gcc -m32 -shared -s -static-libgcc -o CGEN.dll tmp.def Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -lgfortran -LD:/biocbld/BBS-2˜1.13-/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/CGEN.buildbin-libdir/CGEN/libs/i386
** R
** data
** exec
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'CGEN' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Additive.c -o Additive.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c CML.c -o CML.o
CML.c:1198:13: warning: 'print_dVec' defined but not used [-Wunused-function]
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ccl.c -o ccl.o
ccl.c: In function 'ccl_optim':
ccl.c:78:2: warning: passing argument 1 of 'Rf_error' makes pointer from integer without a cast [enabled by default]
D:/biocbld/BBS-2˜1.13-/R/include/R_ext/Error.h:33:6: note: expected 'const char *' but argument is of type 'int'
ccl.c: In function 'factorial':
ccl.c:478:2: warning: passing argument 1 of 'Rf_error' makes pointer from integer without a cast [enabled by default]
D:/biocbld/BBS-2˜1.13-/R/include/R_ext/Error.h:33:6: note: expected 'const char *' but argument is of type 'int'
ccl.c: At top level:
ccl.c:386:13: warning: 'tree_print' defined but not used [-Wunused-function]
gfortran -m64     -O2  -mtune=core2 -c csclust.f -o csclust.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c fsclust.c -o fsclust.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c hcl.c -o hcl.o
hcl.c: In function 'hcl_optim':
hcl.c:72:2: warning: passing argument 1 of 'Rf_error' makes pointer from integer without a cast [enabled by default]
D:/biocbld/BBS-2˜1.13-/R/include/R_ext/Error.h:33:6: note: expected 'const char *' but argument is of type 'int'
hcl.c: In function 'factorial':
hcl.c:467:2: warning: passing argument 1 of 'Rf_error' makes pointer from integer without a cast [enabled by default]
D:/biocbld/BBS-2˜1.13-/R/include/R_ext/Error.h:33:6: note: expected 'const char *' but argument is of type 'int'
hcl.c: At top level:
hcl.c:375:13: warning: 'tree_print' defined but not used [-Wunused-function]
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c pmatch.c -o pmatch.o
gcc -m64 -shared -s -static-libgcc -o CGEN.dll tmp.def Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -lgfortran -LD:/biocbld/BBS-2˜1.13-/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/CGEN.buildbin-libdir/CGEN/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CGEN' as CGEN_2.4.0.zip
* DONE (CGEN)

CGEN.Rcheck/examples_i386/CGEN-Ex.timings:

nameusersystemelapsed
LocusMapData0.040.000.03
QQ.plot000
SNPdata0.010.000.02
Xdata0.020.000.01
additive.test0.920.000.92
chromosome.plot0.140.020.15
getMatchedSets27.46 0.2327.69
getSummary0.000.020.02
getWaldTest0.020.000.01
printEffects0.150.000.16
recode.geno0.020.000.02
snp.effects0.140.000.14
snp.effects.plot0.590.000.59
snp.list000
snp.logistic0.260.000.26
snp.matched23.21 0.0023.21
snp.scan.logistic0.040.000.03

CGEN.Rcheck/examples_x64/CGEN-Ex.timings:

nameusersystemelapsed
LocusMapData0.050.000.04
QQ.plot0.000.020.02
SNPdata0.040.000.05
Xdata0.020.010.03
additive.test1.120.021.14
chromosome.plot0.20.00.2
getMatchedSets28.42 0.1428.56
getSummary0.010.000.01
getWaldTest0.020.000.02
printEffects0.220.000.22
recode.geno0.010.000.01
snp.effects0.240.000.24
snp.effects.plot0.720.010.73
snp.list000
snp.logistic0.300.000.29
snp.matched20.56 0.0020.56
snp.scan.logistic0.030.000.03