Yang Du
| Snapshot Date: 2025-10-12 13:45 -0400 (Sun, 12 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/biomvRCNS |
| git_branch: devel |
| git_last_commit: 4524de5 |
| git_last_commit_date: 2025-04-15 13:25:47 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-13 12:07 -0400 (Mon, 13 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
| 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 218/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biomvRCNS 1.49.0 (landing page) Yang Du
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: biomvRCNS |
| Version: 1.49.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:biomvRCNS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biomvRCNS_1.49.0.tar.gz |
| StartedAt: 2025-10-10 06:33:01 -0000 (Fri, 10 Oct 2025) |
| EndedAt: 2025-10-10 06:49:40 -0000 (Fri, 10 Oct 2025) |
| EllapsedTime: 998.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biomvRCNS.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:biomvRCNS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biomvRCNS_1.49.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/biomvRCNS.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biomvRCNS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biomvRCNS’ version ‘1.49.0’
* 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 ‘biomvRCNS’ can be installed ... OK
* used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* 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 9.006 1.297 6.313
biomvRGviz 5.383 0.179 5.580
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/biomvRCNS.Rcheck/00check.log’
for details.
biomvRCNS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL biomvRCNS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘biomvRCNS’ ... ** this is package ‘biomvRCNS’ version ‘1.49.0’ ** using staged installation ** libs using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c biomvRCNS.c -o biomvRCNS.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o biomvRCNS.so biomvRCNS.o -L/home/biocbuild/R/R-4.5.0/lib -lR installing to /home/biocbuild/R/R-4.5.0/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)
biomvRCNS.Rcheck/biomvRCNS-Ex.timings
| name | user | system | elapsed | |
| biomvRCNS-class | 0.000 | 0.000 | 0.001 | |
| biomvRGviz | 5.383 | 0.179 | 5.580 | |
| biomvRhsmm | 9.006 | 1.297 | 6.313 | |
| biomvRmgmr | 0.628 | 0.069 | 0.699 | |
| biomvRseg | 4.176 | 0.040 | 4.227 | |
| hsmmRun | 0.142 | 0.000 | 0.142 | |
| maxGapminRun | 0.005 | 0.000 | 0.005 | |
| regionSegAlphaNB | 0.104 | 0.000 | 0.105 | |
| regionSegCost | 0.001 | 0.000 | 0.001 | |
| simSegData | 0.002 | 0.000 | 0.003 | |
| sojournAnno | 0.050 | 0.000 | 0.051 | |
| splitFarNeighbour | 0.002 | 0.000 | 0.003 | |