Wei Sun
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/genoCN |
| Branch: RELEASE_3_11 |
| Last Commit: 22c4c2f |
| Last Changed Date: 2020-04-27 14:21:32 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:39 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE genoCN PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 700/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| genoCN 1.40.0 Wei Sun
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: genoCN |
| Version: 1.40.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genoCN.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings genoCN_1.40.0.tar.gz |
| StartedAt: 2020-10-17 04:23:00 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 04:24:39 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 98.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: genoCN.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genoCN.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings genoCN_1.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/genoCN.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'genoCN/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genoCN' version '1.40.0'
* 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 'genoCN' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
genoCNA: no visible binding for global variable 'init.Para.CNA'
genoCNV: no visible binding for global variable 'init.Para.CNV'
Undefined global functions or variables:
init.Para.CNA init.Para.CNV
* 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-3.11-bioc/R/library/genoCN/libs/i386/genoCN.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/genoCN/libs/x64/genoCN.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, 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 (user + system) or elapsed time > 5s
user system elapsed
genoCNA 14.92 0.72 15.86
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
genoCNA 17.25 1.06 18.32
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/genoCN.Rcheck/00check.log'
for details.
genoCN.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/genoCN_1.40.0.tar.gz && rm -rf genoCN.buildbin-libdir && mkdir genoCN.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genoCN.buildbin-libdir genoCN_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL genoCN_1.40.0.zip && rm genoCN_1.40.0.tar.gz genoCN_1.40.0.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 739k 100 739k 0 0 11.5M 0 --:--:-- --:--:-- --:--:-- 12.8M
install for i386
* installing *source* package 'genoCN' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tnorm_mle.c -o tnorm_mle.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utility.c -o utility.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c xCNV.c -o xCNV.o
xCNV.c: In function 'emiss':
xCNV.c:317:25: warning: unused variable 'k' [-Wunused-variable]
int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
^
xCNV.c:317:16: warning: unused variable 'K' [-Wunused-variable]
int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
^
xCNV.c: In function 'baum_welch':
xCNV.c:787:20: warning: unused variable 'sd_b_tmp' [-Wunused-variable]
double mu_b_tmp, sd_b_tmp;
^~~~~~~~
xCNV.c:787:10: warning: unused variable 'mu_b_tmp' [-Wunused-variable]
double mu_b_tmp, sd_b_tmp;
^~~~~~~~
xCNV.c:762:10: warning: variable 'LL' set but not used [-Wunused-but-set-variable]
int L, LL, N, NN, M, MM, S, LS, CNA = *RCNA,
^~
xCNV.c:1839:17: warning: 'nGtp' may be used uninitialized in this function [-Wmaybe-uninitialized]
weights(ws, pbf, z, CNA, contam, nGtp, *geno_error);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
xCNV.c:1839:17: warning: 'pbf' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o genoCN.dll tmp.def tnorm_mle.o utility.o xCNV.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/genoCN.buildbin-libdir/00LOCK-genoCN/00new/genoCN/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'genoCN'
finding HTML links ... done
code.genotype html
genoCNA html
genoCNV html
init.Para.CNA html
init.Para.CNV html
plotCN html
snpData html
snpInfo 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 'genoCN' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tnorm_mle.c -o tnorm_mle.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utility.c -o utility.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c xCNV.c -o xCNV.o
xCNV.c: In function 'emiss':
xCNV.c:317:25: warning: unused variable 'k' [-Wunused-variable]
int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
^
xCNV.c:317:16: warning: unused variable 'K' [-Wunused-variable]
int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
^
xCNV.c: In function 'baum_welch':
xCNV.c:787:20: warning: unused variable 'sd_b_tmp' [-Wunused-variable]
double mu_b_tmp, sd_b_tmp;
^~~~~~~~
xCNV.c:787:10: warning: unused variable 'mu_b_tmp' [-Wunused-variable]
double mu_b_tmp, sd_b_tmp;
^~~~~~~~
xCNV.c:762:10: warning: variable 'LL' set but not used [-Wunused-but-set-variable]
int L, LL, N, NN, M, MM, S, LS, CNA = *RCNA,
^~
xCNV.c:1839:17: warning: 'nGtp' may be used uninitialized in this function [-Wmaybe-uninitialized]
weights(ws, pbf, z, CNA, contam, nGtp, *geno_error);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
xCNV.c:1839:17: warning: 'pbf' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o genoCN.dll tmp.def tnorm_mle.o utility.o xCNV.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/genoCN.buildbin-libdir/genoCN/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genoCN' as genoCN_1.40.0.zip
* DONE (genoCN)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'genoCN' successfully unpacked and MD5 sums checked
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genoCN.Rcheck/examples_i386/genoCN-Ex.timings
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genoCN.Rcheck/examples_x64/genoCN-Ex.timings
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