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This page was generated on 2022-01-19 13:06:44 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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

CHECK results for HMMcopy on tokay2


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? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 881/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HMMcopy 1.36.0  (landing page)
Daniel Lai , Sohrab Shah
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 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 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

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: 2022-01-18 21:01:37 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 21:02:46 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 69.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: HMMcopy.Rcheck
Warnings: 1

Command output

##############################################################################
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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
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/HMMcopy.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 7.01   0.31    7.62
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
HMMcopy-package 5.92   0.19    6.28
* 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.



Installation output

HMMcopy.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


  % 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  588k  100  588k    0     0  2498k      0 --:--:-- --:--:-- --:--:-- 2504k

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

Tests output


Example timings

HMMcopy.Rcheck/examples_i386/HMMcopy-Ex.timings

nameusersystemelapsed
HMMcopy-input0.030.000.03
HMMcopy-output0.340.080.86
HMMcopy-package7.010.317.62
HMMcopy-visualize2.430.052.47
HMMsegment0.170.000.18
correctReadcount0.230.000.23
wigsToRangedData0.060.000.06

HMMcopy.Rcheck/examples_x64/HMMcopy-Ex.timings

nameusersystemelapsed
HMMcopy-input0.030.000.03
HMMcopy-output0.190.030.22
HMMcopy-package5.920.196.28
HMMcopy-visualize2.170.022.88
HMMsegment0.160.000.15
correctReadcount0.090.000.10
wigsToRangedData0.030.000.03