Peng Ni
| Snapshot Date: 2019-12-18 16:46:09 -0500 (Wed, 18 Dec 2019) |
| URL: https://git.bioconductor.org/packages/dSimer |
| Branch: RELEASE_3_10 |
| Last Commit: 34f87d4 |
| Last Changed Date: 2019-10-29 13:09:41 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2019-12-19 12:56:09 -0500 (Thu, 19 Dec 2019).
| Package 488/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Peng Ni
| malbec1 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: dSimer |
| Version: 1.12.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dSimer.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings dSimer_1.12.0.tar.gz |
| StartedAt: 2019-12-19 03:18:13 -0500 (Thu, 19 Dec 2019) |
| EndedAt: 2019-12-19 03:25:29 -0500 (Thu, 19 Dec 2019) |
| EllapsedTime: 435.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: dSimer.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dSimer.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings dSimer_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/dSimer.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'dSimer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dSimer' version '1.12.0'
* 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 'dSimer' can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'dSimer' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/dSimer.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
data 3.1Mb
libs 1.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 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/dSimer/libs/i386/dSimer.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/dSimer/libs/x64/dSimer.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
get_GOterm2GeneAssos 37.78 2.31 40.14
plot_heatmap 18.10 0.30 18.39
FunSim 17.22 0.13 17.34
plot_net 17.06 0.25 17.31
Separation 13.56 0.28 13.85
PSB 9.94 0.00 9.93
HypergeometricTest 8.84 0.07 8.92
BOG 5.28 0.08 5.40
x2y_conv2_y2x 5.14 0.02 5.15
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
get_GOterm2GeneAssos 38.64 1.83 40.47
plot_net 15.08 0.32 15.41
FunSim 15.06 0.18 15.24
plot_heatmap 14.25 0.33 14.57
PSB 13.29 0.01 13.29
HypergeometricTest 12.97 0.12 13.09
Separation 8.81 0.30 9.11
x2y_conv2_y2x 8.84 0.00 8.85
BOG 5.49 0.10 5.77
* 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: 1 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/dSimer.Rcheck/00check.log'
for details.
dSimer.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/dSimer_1.12.0.tar.gz && rm -rf dSimer.buildbin-libdir && mkdir dSimer.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=dSimer.buildbin-libdir dSimer_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL dSimer_1.12.0.zip && rm dSimer_1.12.0.tar.gz dSimer_1.12.0.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 3193k 100 3193k 0 0 24.1M 0 --:--:-- --:--:-- --:--:-- 24.7M
install for i386
* installing *source* package 'dSimer' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c BOG.cpp -o BOG.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c GO2GeneAssos.cpp -o GO2GeneAssos.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ICod.cpp -o ICod.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c PSB.cpp -o PSB.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c R_dSimer_init.c -o R_dSimer_init.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Sun.cpp -o Sun.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o dSimer.dll tmp.def BOG.o GO2GeneAssos.o ICod.o PSB.o R_dSimer_init.o RcppExports.o Sun.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/dSimer.buildbin-libdir/00LOCK-dSimer/00new/dSimer/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'dSimer'
finding HTML links ... done
BOG html
CosineDFV html
FunSim html
HumanNet_sample html
HypergeometricTest html
ICod html
InformationContent html
LLSn2List html
Normalize html
PPI_HPRD html
PSB html
Separation html
Separation2Similarity html
Sun_annotation html
Sun_function html
Sun_topology html
d2g_fundo_entrezid html
d2g_fundo_symbol html
d2g_separation html
d2go_sample html
d2s_hsdn html
d2s_hsdn_sample html
dSimer-package html
get_GOterm2GeneAssos html
go2g_sample html
graphlet_sig_hprd html
interactome html
jaccardindex html
orbit_dependency_count html
plot_bipartite html
plot_heatmap html
plot_net html
plot_topo html
setWeight html
weight html
x2y_conv2_y2x html
x2y_df2list html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'dSimer' is deprecated and will be removed from Bioconductor
version 3.11
** testing if installed package can be loaded from final location
Warning: Package 'dSimer' is deprecated and will be removed from Bioconductor
version 3.11
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'dSimer' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c BOG.cpp -o BOG.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c GO2GeneAssos.cpp -o GO2GeneAssos.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ICod.cpp -o ICod.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c PSB.cpp -o PSB.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c R_dSimer_init.c -o R_dSimer_init.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Sun.cpp -o Sun.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o dSimer.dll tmp.def BOG.o GO2GeneAssos.o ICod.o PSB.o R_dSimer_init.o RcppExports.o Sun.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/dSimer.buildbin-libdir/dSimer/libs/x64
** testing if installed package can be loaded
Warning: Package 'dSimer' is deprecated and will be removed from Bioconductor
version 3.11
* MD5 sums
packaged installation of 'dSimer' as dSimer_1.12.0.zip
* DONE (dSimer)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'dSimer' successfully unpacked and MD5 sums checked
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dSimer.Rcheck/examples_i386/dSimer-Ex.timings
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dSimer.Rcheck/examples_x64/dSimer-Ex.timings
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