Daniel Lai
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/HMMcopy |
| git_branch: RELEASE_3_14 |
| git_last_commit: b37931c |
| git_last_commit_date: 2021-10-26 12:05:00 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:42 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the HMMcopy package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HMMcopy.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 881/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HMMcopy 1.36.0 (landing page) Daniel Lai
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: HMMcopy |
| Version: 1.36.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HMMcopy.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings HMMcopy_1.36.0.tar.gz |
| StartedAt: 2022-04-12 21:11:26 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 21:12:46 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 79.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: HMMcopy.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HMMcopy.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings HMMcopy_1.36.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/HMMcopy.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.36.0'
* 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 ... OK
* 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 6.22 0.14 6.42
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
HMMcopy-package 6.25 0.22 6.47
* 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
See
'C:/Users/biocbuild/bbs-3.14-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://155.52.207.166/BBS/3.14/bioc/src/contrib/HMMcopy_1.36.0.tar.gz && rm -rf HMMcopy.buildbin-libdir && mkdir HMMcopy.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HMMcopy.buildbin-libdir HMMcopy_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL HMMcopy_1.36.0.zip && rm HMMcopy_1.36.0.tar.gz HMMcopy_1.36.0.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
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 588k 100 588k 0 0 745k 0 --:--:-- --:--:-- --:--:-- 744k
install for i386
* installing *source* package 'HMMcopy' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/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-3~1.14-/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-3~1.14-/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-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-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
HMMcopy-input html
HMMcopy-internal html
HMMcopy-output html
HMMcopy-package html
HMMcopy-visualize html
HMMsegment html
correctReadcount html
wigsToRangedData 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 'HMMcopy' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/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-3~1.14-/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-3~1.14-/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-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/HMMcopy.buildbin-libdir/HMMcopy/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HMMcopy' as HMMcopy_1.36.0.zip
* DONE (HMMcopy)
* installing to library 'C:/Users/biocbuild/bbs-3.14-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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