| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-25 11:38 -0400 (Thu, 25 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4827 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4581 |
| 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 987/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| hiReadsProcessor 1.44.0 (landing page) Nirav V Malani
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the hiReadsProcessor package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hiReadsProcessor.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. |
| Package: hiReadsProcessor |
| Version: 1.44.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:hiReadsProcessor.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings hiReadsProcessor_1.44.0.tar.gz |
| StartedAt: 2025-09-25 00:30:56 -0400 (Thu, 25 Sep 2025) |
| EndedAt: 2025-09-25 00:36:00 -0400 (Thu, 25 Sep 2025) |
| EllapsedTime: 304.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: hiReadsProcessor.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:hiReadsProcessor.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings hiReadsProcessor_1.44.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/hiReadsProcessor.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘hiReadsProcessor/DESCRIPTION’ ... OK
* this is package ‘hiReadsProcessor’ version ‘1.44.0’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘hiReadsProcessor’ 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 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
chunkize: no visible global function definition for ‘breakInChunks’
chunkize: no visible global function definition for ‘detectCores’
clusterSites : <anonymous>: no visible binding for global variable
‘queryHits’
clusterSites: no visible binding for global variable ‘clusteredValue’
clusterSites: no visible binding for global variable
‘clusteredValue.freq’
crossOverCheck: no visible binding for global variable ‘queryHits’
decodeByBarcode: no visible global function definition for ‘metadata<-’
decodeByBarcode: no visible global function definition for ‘metadata’
extractSeqs : <anonymous>: no visible global function definition for
‘metadata’
extractSeqs : <anonymous> : <anonymous> : <anonymous>: no visible
global function definition for ‘IRanges’
extractSeqs : <anonymous> : <anonymous>: no visible global function
definition for ‘IRanges’
findBarcodes: no visible global function definition for ‘metadata<-’
findBarcodes: no visible global function definition for ‘metadata’
findIntegrations: no visible global function definition for
‘fasta.info’
findIntegrations : <anonymous>: no visible global function definition
for ‘IRanges’
findVector : <anonymous>: no visible global function definition for
‘IRanges’
pairUpAlignments : <anonymous>: no visible binding for global variable
‘queryHits’
pairwiseAlignSeqs: no visible global function definition for
‘IRangesList’
pairwiseAlignSeqs: no visible global function definition for ‘IRanges’
primerIDAlignSeqs: no visible global function definition for ‘IRanges’
primerIDAlignSeqs: no visible global function definition for
‘IRangesList’
pslToRangedObject: no visible global function definition for ‘IRanges’
read.BAMasPSL: no visible global function definition for ‘ScanBamParam’
read.BAMasPSL: no visible global function definition for ‘scanBamFlag’
read.BAMasPSL: no visible global function definition for ‘DataFrame’
read.SeqFolder: no visible global function definition for ‘SimpleList’
read.psl: no visible global function definition for ‘mclapply’
read.psl : <anonymous>: no visible binding for global variable
‘matches’
read.psl : <anonymous>: no visible binding for global variable
‘misMatches’
read.psl : <anonymous>: no visible binding for global variable
‘qBaseInsert’
read.psl : <anonymous>: no visible binding for global variable
‘tBaseInsert’
read.psl: no visible binding for global variable ‘matches’
read.psl: no visible binding for global variable ‘misMatches’
read.psl: no visible binding for global variable ‘qBaseInsert’
read.psl: no visible binding for global variable ‘tBaseInsert’
read.sampleInfo: no visible global function definition for ‘SimpleList’
splitSeqsToFiles: no visible global function definition for
‘fasta.info’
vpairwiseAlignSeqs: no visible global function definition for ‘Rle’
vpairwiseAlignSeqs: no visible global function definition for
‘runLength’
vpairwiseAlignSeqs: no visible global function definition for ‘IRanges’
vpairwiseAlignSeqs: no visible global function definition for
‘runValue’
Undefined global functions or variables:
DataFrame IRanges IRangesList Rle ScanBamParam SimpleList
breakInChunks clusteredValue clusteredValue.freq detectCores
fasta.info matches mclapply metadata metadata<- misMatches
qBaseInsert queryHits runLength runValue scanBamFlag tBaseInsert
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
annotateSites.Rd: SerialParam, doAnnotation
blatSeqs.Rd: BiocParallel, SerialParam
clusterSites.Rd: BiocParallel, SerialParam
doRCtest.Rd: vcountPattern, BiocParallel, SerialParam
findAndRemoveVector.Rd: BiocParallel, SerialParam, MulticoreParam,
SnowParam
findAndTrimSeq.Rd: vmatchPattern, pairwiseAlignment, MulticoreParam,
SnowParam
findIntegrations.Rd: BiocParallel, SerialParam, MulticoreParam,
SnowParam
findLTRs.Rd: BiocParallel, SerialParam, pairwiseAlignment,
MulticoreParam, SnowParam
findLinkers.Rd: BiocParallel, SerialParam, pairwiseAlignment,
MulticoreParam, SnowParam
findPrimers.Rd: vmatchPattern, pairwiseAlignment, SerialParam,
MulticoreParam, SnowParam
findVector.Rd: BiocParallel, SerialParam, MulticoreParam, SnowParam
getSonicAbund.Rd: sonicLength, BiocParallel, SerialParam
isuSites.Rd: BiocParallel, SerialParam
otuSites.Rd: BiocParallel, SerialParam
pairUpAlignments.Rd: BiocParallel, SerialParam
pairwiseAlignSeqs.Rd: pairwiseAlignment, BiocParallel, SerialParam,
MulticoreParam, SnowParam
primerIDAlignSeqs.Rd: pairwiseAlignment
read.blast8.Rd: BiocParallel, SerialParam, MulticoreParam, SnowParam
read.psl.Rd: BiocParallel, SerialParam, MulticoreParam, SnowParam
troubleshootLinkers.Rd: BiocParallel, SerialParam, pairwiseAlignment,
MulticoreParam, SnowParam
vpairwiseAlignSeqs.Rd: vmatchPattern, BiocParallel, SerialParam,
MulticoreParam, SnowParam
write.listedDNAStringSet.Rd: BiocParallel, SerialParam,
writeXStringSet, MulticoreParam, SnowParam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/hiReadsProcessor.Rcheck/00check.log’
for details.
hiReadsProcessor.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL hiReadsProcessor ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘hiReadsProcessor’ ... ** this is package ‘hiReadsProcessor’ version ‘1.44.0’ ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (hiReadsProcessor)
hiReadsProcessor.Rcheck/hiReadsProcessor-Ex.timings
| name | user | system | elapsed | |
| addFeature | 0.170 | 0.026 | 0.194 | |
| addListNameToReads | 0.242 | 0.005 | 0.245 | |
| annotateSites | 0 | 0 | 0 | |
| blatSeqs | 0 | 0 | 0 | |
| chunkize | 0.027 | 0.000 | 0.029 | |
| clusterSites | 0.283 | 0.000 | 0.285 | |
| crossOverCheck | 0.091 | 0.001 | 0.094 | |
| dereplicateReads | 0.036 | 0.000 | 0.037 | |
| doRCtest | 3.708 | 0.071 | 3.797 | |
| extractFeature | 0.145 | 0.110 | 0.133 | |
| extractSeqs | 0.373 | 0.037 | 0.412 | |
| findAndTrimSeq | 1.350 | 0.183 | 1.534 | |
| findBarcodes | 0.966 | 0.067 | 1.034 | |
| findIntegrations | 0.000 | 0.000 | 0.001 | |
| findLTRs | 0 | 0 | 0 | |
| findLinkers | 0 | 0 | 0 | |
| findPrimers | 0 | 0 | 0 | |
| findVector | 0 | 0 | 0 | |
| getIntegrationSites | 2.090 | 0.243 | 2.332 | |
| getSectorsForSamples | 0.083 | 0.005 | 0.088 | |
| getSonicAbund | 0.323 | 0.221 | 0.496 | |
| isuSites | 4.337 | 0.508 | 4.846 | |
| otuSites | 4.339 | 0.358 | 4.698 | |
| pairUpAlignments | 0.000 | 0.000 | 0.001 | |
| pairwiseAlignSeqs | 2.200 | 0.759 | 2.810 | |
| primerIDAlignSeqs | 3.063 | 0.380 | 3.352 | |
| pslCols | 0.000 | 0.001 | 0.001 | |
| pslToRangedObject | 0.161 | 0.003 | 0.164 | |
| read.BAMasPSL | 0.000 | 0.001 | 0.000 | |
| read.SeqFolder | 0.929 | 0.033 | 0.963 | |
| read.blast8 | 0 | 0 | 0 | |
| read.psl | 0 | 0 | 0 | |
| read.sampleInfo | 0.952 | 0.009 | 0.961 | |
| read.seqsFromSector | 0 | 0 | 0 | |
| removeReadsWithNs | 0.020 | 0.001 | 0.020 | |
| replicateReads | 0.045 | 0.002 | 0.047 | |
| sampleSummary | 0.576 | 0.019 | 0.596 | |
| splitByBarcode | 0.028 | 0.002 | 0.030 | |
| splitSeqsToFiles | 0.127 | 0.004 | 0.130 | |
| startgfServer | 0 | 0 | 0 | |
| trimSeqs | 0.022 | 0.002 | 0.023 | |
| vpairwiseAlignSeqs | 2.439 | 1.082 | 3.322 | |
| write.listedDNAStringSet | 0.001 | 0.000 | 0.000 | |
| write.psl | 0.018 | 0.002 | 0.021 | |