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This page was generated on 2024-03-28 11:36:14 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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

Package 211/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biomvRCNS 1.43.1  (landing page)
Yang Du
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/biomvRCNS
git_branch: devel
git_last_commit: 5dee23f
git_last_commit_date: 2023-12-19 22:47:27 -0400 (Tue, 19 Dec 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for biomvRCNS on nebbiolo1


To the developers/maintainers of the biomvRCNS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biomvRCNS.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: biomvRCNS
Version: 1.43.1
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biomvRCNS.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biomvRCNS_1.43.1.tar.gz
StartedAt: 2024-03-27 20:41:26 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 20:47:53 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 386.4 seconds
RetCode: 0
Status:   OK  
CheckDir: biomvRCNS.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biomvRCNS.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biomvRCNS_1.43.1.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/biomvRCNS.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘biomvRCNS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biomvRCNS’ version ‘1.43.1’
* 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 ‘biomvRCNS’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 code 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 ... NOTE
'library' or 'require' calls in package code:
  'GenomicFeatures' 'cluster' 'dynamicTreeCut' 'parallel'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
biomvRGviz: no visible global function definition for 'rainbow'
biomvRGviz: no visible global function definition for 'hasArg'
biomvRGviz: no visible global function definition for 'graphics.off'
biomvRGviz: no visible global function definition for 'setEPS'
biomvRGviz: no visible global function definition for 'postscript'
biomvRGviz: no visible global function definition for 'pdf'
biomvRGviz: no visible global function definition for 'dev.off'
biomvRhsmm: no visible global function definition for 'is'
biomvRhsmm: no visible binding for global variable 'mclapply'
biomvRhsmm : <anonymous> : <anonymous>: no visible global function
  definition for 'DataFrame'
biomvRhsmm : <anonymous> : <anonymous>: no visible global function
  definition for 'Rle'
biomvRhsmm: no visible global function definition for 'DataFrame'
biomvRhsmm: no visible binding for global variable 'DataFrame'
biomvRhsmm: no visible global function definition for 'new'
biomvRmgmr: no visible global function definition for 'seqlevels<-'
biomvRmgmr: no visible global function definition for 'DataFrame'
biomvRmgmr: no visible global function definition for 'new'
biomvRseg: no visible global function definition for 'seqlevels<-'
biomvRseg: no visible global function definition for 'DataFrame'
biomvRseg: no visible global function definition for 'new'
estEmis: no visible global function definition for 'clara'
gammaFit: no visible global function definition for 'cov.wt'
hsmmRun: no visible global function definition for 'Rle'
hsmmRun : <anonymous>: no visible global function definition for 'Rle'
hsmmRun: no visible global function definition for 'seqlevels<-'
initEmis : <anonymous>: no visible global function definition for
  'dpois'
initEmis : <anonymous>: no visible global function definition for
  'dnorm'
initEmis : <anonymous>: no visible global function definition for
  'dnbinom'
initEmis : <anonymous>: no visible global function definition for
  'cov2cor'
initEmis : <anonymous>: no visible global function definition for 'dt'
initEmis : <anonymous>: no visible global function definition for
  'cov.wt'
initEmis : <anonymous>: no visible global function definition for
  'weighted.mean'
initSojDd : <anonymous>: no visible global function definition for
  'dgamma'
initSojDd : <anonymous>: no visible global function definition for
  'dpois'
initSojDd : <anonymous>: no visible global function definition for
  'dnbinom'
maxGapminRun: no visible global function definition for 'Rle'
maxGapminRun: no visible global function definition for 'runValue'
nbinomCLLDD: no visible global function definition for 'cov.wt'
nbinomCLLDD: no visible global function definition for 'dnbinom'
poisFit : <anonymous>: no visible global function definition for
  'dpois'
preClustGrp: no visible global function definition for 'dist'
preClustGrp: no visible global function definition for 'hclust'
preClustGrp: no visible global function definition for 'cutreeDynamic'
regionSegAlphaNB: no visible global function definition for 'mclapply'
regionSegCost: no visible global function definition for 'mclapply'
simSegData: no visible global function definition for 'runValue'
simSegData: no visible global function definition for 'Rle'
simSegData: no visible global function definition for 'pdf'
simSegData: no visible global function definition for 'ts.plot'
simSegData: no visible global function definition for 'dev.off'
simUvSegData: no visible global function definition for 'rnorm'
simUvSegData: no visible global function definition for 'rt'
simUvSegData: no visible global function definition for 'rgamma'
simUvSegData: no visible global function definition for 'rpois'
simUvSegData: no visible global function definition for 'rnbinom'
sojournAnno: no visible global function definition for 'is'
sojournAnno: no visible global function definition for 'transcripts'
sojournAnno: no visible global function definition for 'seqlengths'
sojournAnno: no visible global function definition for 'exons'
sojournAnno: no visible global function definition for
  'intronsByTranscript'
splitFarNeighbouryhat: no visible global function definition for
  'runValue'
tmvtfFit: no visible global function definition for 'cov.wt'
unifMJ : <anonymous>: no visible global function definition for 'dunif'
unifMJ : <anonymous> : <anonymous>: no visible global function
  definition for 'dunif'
plot,biomvRCNS-ANY: no visible binding for global variable 'ssetst'
Undefined global functions or variables:
  DataFrame Rle clara cov.wt cov2cor cutreeDynamic dev.off dgamma dist
  dnbinom dnorm dpois dt dunif exons graphics.off hasArg hclust
  intronsByTranscript is mclapply new pdf postscript rainbow rgamma
  rnbinom rnorm rpois rt runValue seqlengths seqlevels<- setEPS ssetst
  transcripts ts.plot weighted.mean
Consider adding
  importFrom("grDevices", "dev.off", "graphics.off", "pdf", "postscript",
             "rainbow", "setEPS")
  importFrom("methods", "hasArg", "is", "new")
  importFrom("stats", "cov.wt", "cov2cor", "dgamma", "dist", "dnbinom",
             "dnorm", "dpois", "dt", "dunif", "hclust", "rgamma",
             "rnbinom", "rnorm", "rpois", "rt", "ts.plot",
             "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) sojournAnno.Rd:32: Lost braces
    32 | \item{\\code{...}}{distribution parameters, 'lambda' and 'shift' for 'pois'; 'size', 'mu' and 'shift' for 'nbinom'; 'scale' and 'shape' for 'gamma'}
       |             ^
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
biomvRhsmm 5.717  1.128   4.058
biomvRGviz 5.452  0.631   6.085
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/biomvRCNS.Rcheck/00check.log’
for details.


Installation output

biomvRCNS.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL biomvRCNS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘biomvRCNS’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c biomvRCNS.c -o biomvRCNS.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o biomvRCNS.so biomvRCNS.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-biomvRCNS/00new/biomvRCNS/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 (biomvRCNS)

Tests output


Example timings

biomvRCNS.Rcheck/biomvRCNS-Ex.timings

nameusersystemelapsed
biomvRCNS-class0.0020.0000.001
biomvRGviz5.4520.6316.085
biomvRhsmm5.7171.1284.058
biomvRmgmr0.3760.0080.384
biomvRseg2.7620.0722.835
hsmmRun0.0790.0000.079
maxGapminRun0.0040.0000.003
regionSegAlphaNB0.0510.0000.050
regionSegCost0.0000.0000.001
simSegData0.0050.0000.006
sojournAnno0.0310.0000.031
splitFarNeighbour0.0020.0000.002