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This page was generated on 2023-04-12 11:05:07 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 nebbiolo2


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.

raw results

Package 921/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HMMcopy 1.40.0  (landing page)
Daniel Lai
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/HMMcopy
git_branch: RELEASE_3_16
git_last_commit: 47a99fe
git_last_commit_date: 2022-11-01 11:07:29 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: HMMcopy
Version: 1.40.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:HMMcopy.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings HMMcopy_1.40.0.tar.gz
StartedAt: 2023-04-10 21:18:10 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 21:18:50 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 40.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: HMMcopy.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:HMMcopy.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings HMMcopy_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/HMMcopy.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘HMMcopy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HMMcopy’ 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 for sufficient/correct file permissions ... 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
* 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 loading without being on the library search path ... 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
rangedDataToWig: no visible binding for global variable ‘chr’
Undefined global functions or variables:
  chr
* 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 ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘HMMcopy.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/HMMcopy.Rcheck/00check.log’
for details.



Installation output

HMMcopy.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL HMMcopy
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘HMMcopy’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -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]
   28 |   int K, T, tmp;
      |             ^~~
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c register.c -o register.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c viterbi.c -o viterbi.o
viterbi.c: In function ‘viterbi’:
viterbi.c:21:13: warning: unused variable ‘tmp’ [-Wunused-variable]
   21 |   int K, T, tmp;
      |             ^~~
gcc -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o HMMcopy.so forward_backward.o register.o viterbi.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-HMMcopy/00new/HMMcopy/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HMMcopy)

Tests output


Example timings

HMMcopy.Rcheck/HMMcopy-Ex.timings

nameusersystemelapsed
HMMcopy-input0.0140.0080.021
HMMcopy-output0.1190.0080.127
HMMcopy-package4.1020.1204.196
HMMcopy-visualize1.6300.0161.628
HMMsegment0.0980.0040.102
correctReadcount0.1050.0000.105
wigsToRangedData0.0320.0000.032