Daniel Lai
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/HMMcopy |
| Branch: RELEASE_3_12 |
| Last Commit: ba30e1f |
| Last Changed Date: 2020-10-27 10:47:39 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:31:46 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the HMMcopy package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 844/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HMMcopy 1.32.0 (landing page) Daniel Lai
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: HMMcopy |
| Version: 1.32.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HMMcopy.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings HMMcopy_1.32.0.tar.gz |
| StartedAt: 2021-05-06 03:40:06 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 03:41:19 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 72.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: HMMcopy.Rcheck |
| Warnings: 2 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HMMcopy.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings HMMcopy_1.32.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/HMMcopy.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HMMcopy/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HMMcopy' version '1.32.0'
* 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 'HMMcopy' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpILPuqR/R.INSTALLc3c56f32a73/HMMcopy/man/HMMcopy-dataset.Rd:41: missing file link 'RangedData-class'
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpILPuqR/R.INSTALLc3c56f32a73/HMMcopy/man/HMMcopy-input.Rd:32: missing file link 'RangedData-class'
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpILPuqR/R.INSTALLc3c56f32a73/HMMcopy/man/HMMcopy-output.Rd:18: missing file link 'RangedData-class'
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpILPuqR/R.INSTALLc3c56f32a73/HMMcopy/man/correctReadcount.Rd:15: missing file link 'RangedData-class'
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpILPuqR/R.INSTALLc3c56f32a73/HMMcopy/man/correctReadcount.Rd:59: missing file link 'RangedData-class'
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpILPuqR/R.INSTALLc3c56f32a73/HMMcopy/man/wigsToRangedData.Rd:41: missing file link 'RangedData-class'
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/HMMcopy.Rcheck/00install.out' for details.
* checking installed package size ... OK
* 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 ... WARNING
Missing link or links in documentation object 'HMMcopy-dataset.Rd':
'[IRanges:RangedData-class]{RangedData}'
Missing link or links in documentation object 'HMMcopy-input.Rd':
'[IRanges:RangedData-class]{RangedData}'
Missing link or links in documentation object 'HMMcopy-output.Rd':
'[IRanges:RangedData-class]{RangedData}'
Missing link or links in documentation object 'correctReadcount.Rd':
'[IRanges:RangedData-class]{RangedData}'
Missing link or links in documentation object 'wigsToRangedData.Rd':
'[IRanges:RangedData-class]{RangedData}'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ... OK
* 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
HMMcopy-package 6.75 0.22 7.22
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
HMMcopy-package 6.29 0.19 7.02
* 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: 2 WARNINGs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/HMMcopy.Rcheck/00check.log'
for details.
HMMcopy.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/HMMcopy_1.32.0.tar.gz && rm -rf HMMcopy.buildbin-libdir && mkdir HMMcopy.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HMMcopy.buildbin-libdir HMMcopy_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL HMMcopy_1.32.0.zip && rm HMMcopy_1.32.0.tar.gz HMMcopy_1.32.0.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 587k 100 587k 0 0 25.0M 0 --:--:-- --:--:-- --:--:-- 26.0M
install for i386
* installing *source* package 'HMMcopy' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c forward_backward.c -o forward_backward.o
forward_backward.c: In function 'forward_backward':
forward_backward.c:28:13: warning: unused variable 'tmp' [-Wunused-variable]
int K, T, tmp;
^~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c register.c -o register.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c viterbi.c -o viterbi.o
viterbi.c: In function 'viterbi':
viterbi.c:21:13: warning: unused variable 'tmp' [-Wunused-variable]
int K, T, tmp;
^~~
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o HMMcopy.dll tmp.def forward_backward.o register.o viterbi.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/HMMcopy.buildbin-libdir/00LOCK-HMMcopy/00new/HMMcopy/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'HMMcopy'
finding HTML links ... done
HMMcopy-dataset html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpILPuqR/R.INSTALLc3c56f32a73/HMMcopy/man/HMMcopy-dataset.Rd:41: missing file link 'RangedData-class'
HMMcopy-input html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpILPuqR/R.INSTALLc3c56f32a73/HMMcopy/man/HMMcopy-input.Rd:32: missing file link 'RangedData-class'
HMMcopy-internal html
HMMcopy-output html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpILPuqR/R.INSTALLc3c56f32a73/HMMcopy/man/HMMcopy-output.Rd:18: missing file link 'RangedData-class'
HMMcopy-package html
HMMcopy-visualize html
HMMsegment html
correctReadcount html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpILPuqR/R.INSTALLc3c56f32a73/HMMcopy/man/correctReadcount.Rd:15: missing file link 'RangedData-class'
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpILPuqR/R.INSTALLc3c56f32a73/HMMcopy/man/correctReadcount.Rd:59: missing file link 'RangedData-class'
wigsToRangedData html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpILPuqR/R.INSTALLc3c56f32a73/HMMcopy/man/wigsToRangedData.Rd:41: missing file link 'RangedData-class'
** 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 'HMMcopy' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c forward_backward.c -o forward_backward.o
forward_backward.c: In function 'forward_backward':
forward_backward.c:28:13: warning: unused variable 'tmp' [-Wunused-variable]
int K, T, tmp;
^~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c register.c -o register.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c viterbi.c -o viterbi.o
viterbi.c: In function 'viterbi':
viterbi.c:21:13: warning: unused variable 'tmp' [-Wunused-variable]
int K, T, tmp;
^~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o HMMcopy.dll tmp.def forward_backward.o register.o viterbi.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/HMMcopy.buildbin-libdir/HMMcopy/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HMMcopy' as HMMcopy_1.32.0.zip
* DONE (HMMcopy)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'HMMcopy' successfully unpacked and MD5 sums checked
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HMMcopy.Rcheck/examples_i386/HMMcopy-Ex.timings
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HMMcopy.Rcheck/examples_x64/HMMcopy-Ex.timings
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