Greg Imholte
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/iBMQ |
| Branch: RELEASE_3_10 |
| Last Commit: 15769c7 |
| Last Changed Date: 2019-10-29 13:08:36 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:21:14 -0400 (Wed, 15 Apr 2020).
| Package 814/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| iBMQ 1.26.0 Greg Imholte
| 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 | ...NOT SUPPORTED... | ||||||||||
| Package: iBMQ |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iBMQ.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings iBMQ_1.26.0.tar.gz |
| StartedAt: 2020-04-15 03:58:06 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:59:40 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 94.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: iBMQ.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iBMQ.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings iBMQ_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/iBMQ.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 'iBMQ/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iBMQ' version '1.26.0'
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'iBMQ' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Packages in Depends field not imported from:
'Biobase' 'ggplot2'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
eqtlMcmc: no visible global function definition for 'is'
eqtlMcmc: no visible global function definition for 'exprs'
Undefined global functions or variables:
exprs is
Consider adding
importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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 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/iBMQ/libs/i386/iBMQ.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/iBMQ/libs/x64/iBMQ.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
** 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: 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/iBMQ.Rcheck/00check.log'
for details.
iBMQ.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/iBMQ_1.26.0.tar.gz && rm -rf iBMQ.buildbin-libdir && mkdir iBMQ.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iBMQ.buildbin-libdir iBMQ_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL iBMQ_1.26.0.zip && rm iBMQ_1.26.0.tar.gz iBMQ_1.26.0.zip
###
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% 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 3800k 100 3800k 0 0 39.2M 0 --:--:-- --:--:-- --:--:-- 40.7M
install for i386
* installing *source* package 'iBMQ' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/i386/include -fopenmp -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ARS.c -o ARS.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/i386/include -fopenmp -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c RngStream.c -o RngStream.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/i386/include -fopenmp -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c iBMQ_common.c -o iBMQ_common.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/i386/include -fopenmp -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c main_parallel_sparse.c -o main_parallel_sparse.o
main_parallel_sparse.c: In function 'iBMQ_main':
main_parallel_sparse.c:289:3: warning: 'Cfile' may be used uninitialized in this function [-Wmaybe-uninitialized]
fclose(Cfile);
^
main_parallel_sparse.c:288:3: warning: 'Sig2file' may be used uninitialized in this function [-Wmaybe-uninitialized]
fclose(Sig2file);
^
main_parallel_sparse.c:287:3: warning: 'Mufile' may be used uninitialized in this function [-Wmaybe-uninitialized]
fclose(Mufile);
^
main_parallel_sparse.c:285:3: warning: 'Bfile' may be used uninitialized in this function [-Wmaybe-uninitialized]
fclose(Bfile);
^
main_parallel_sparse.c:284:3: warning: 'Afile' may be used uninitialized in this function [-Wmaybe-uninitialized]
fclose(Afile);
^
main_parallel_sparse.c:286:3: warning: 'Pfile' may be used uninitialized in this function [-Wmaybe-uninitialized]
fclose(Pfile);
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/i386/include -fopenmp -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c main_parallel_sparse_constC.c -o main_parallel_sparse_constC.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/i386/include -fopenmp -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c norm_gamma_generation.c -o norm_gamma_generation.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/i386/include -fopenmp -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c sparse.c -o sparse.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o iBMQ.dll tmp.def ARS.o RngStream.o iBMQ_common.o main_parallel_sparse.o main_parallel_sparse_constC.o norm_gamma_generation.o sparse.o -L/i386/lib -lgsl -lgslcblas -lm -fopenmp -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/iBMQ.buildbin-libdir/00LOCK-iBMQ/00new/iBMQ/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'iBMQ'
finding HTML links ... done
PPA.liver html
calculateThreshold html
eqtlClassifier html
eqtlFinder html
eqtlMcmc html
gene html
genepos html
genotype.liver html
hotspotFinder html
iBMQ-package html
map.liver html
phenotype.liver html
probe.liver html
snp html
snppos 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 'iBMQ' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c ARS.c -o ARS.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c RngStream.c -o RngStream.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c iBMQ_common.c -o iBMQ_common.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c main_parallel_sparse.c -o main_parallel_sparse.o
main_parallel_sparse.c: In function 'iBMQ_main':
main_parallel_sparse.c:289:3: warning: 'Cfile' may be used uninitialized in this function [-Wmaybe-uninitialized]
fclose(Cfile);
^
main_parallel_sparse.c:288:3: warning: 'Sig2file' may be used uninitialized in this function [-Wmaybe-uninitialized]
fclose(Sig2file);
^
main_parallel_sparse.c:287:3: warning: 'Mufile' may be used uninitialized in this function [-Wmaybe-uninitialized]
fclose(Mufile);
^
main_parallel_sparse.c:285:3: warning: 'Bfile' may be used uninitialized in this function [-Wmaybe-uninitialized]
fclose(Bfile);
^
main_parallel_sparse.c:284:3: warning: 'Afile' may be used uninitialized in this function [-Wmaybe-uninitialized]
fclose(Afile);
^
main_parallel_sparse.c:286:3: warning: 'Pfile' may be used uninitialized in this function [-Wmaybe-uninitialized]
fclose(Pfile);
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c main_parallel_sparse_constC.c -o main_parallel_sparse_constC.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c norm_gamma_generation.c -o norm_gamma_generation.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c sparse.c -o sparse.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o iBMQ.dll tmp.def ARS.o RngStream.o iBMQ_common.o main_parallel_sparse.o main_parallel_sparse_constC.o norm_gamma_generation.o sparse.o -L/x64/lib -lgsl -lgslcblas -lm -fopenmp -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/iBMQ.buildbin-libdir/iBMQ/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iBMQ' as iBMQ_1.26.0.zip
* DONE (iBMQ)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'iBMQ' successfully unpacked and MD5 sums checked
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iBMQ.Rcheck/examples_i386/iBMQ-Ex.timings
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iBMQ.Rcheck/examples_x64/iBMQ-Ex.timings
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