| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:37:08 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 940/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| hiReadsProcessor 1.36.0 (landing page) Nirav V Malani
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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: 1.36.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:hiReadsProcessor.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings hiReadsProcessor_1.36.0.tar.gz |
| StartedAt: 2023-10-16 02:40:46 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 02:51:14 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 628.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: hiReadsProcessor.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:hiReadsProcessor.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings hiReadsProcessor_1.36.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/hiReadsProcessor.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hiReadsProcessor/DESCRIPTION’ ... OK
* this is package ‘hiReadsProcessor’ 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 ... 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 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 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
isuSites 5.147 0.406 7.179
otuSites 5.420 0.035 7.245
primerIDAlignSeqs 3.710 0.590 5.480
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc/meat/hiReadsProcessor.Rcheck/00check.log’
for details.
hiReadsProcessor.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL hiReadsProcessor ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘hiReadsProcessor’ ... ** 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 | 0.374 | 0.011 | 0.481 | |
| addListNameToReads | 0.541 | 0.014 | 0.707 | |
| annotateSites | 0.000 | 0.000 | 0.001 | |
| blatSeqs | 0.000 | 0.001 | 0.004 | |
| chunkize | 0.065 | 0.004 | 0.090 | |
| clusterSites | 0.787 | 0.018 | 1.022 | |
| crossOverCheck | 0.216 | 0.002 | 0.265 | |
| dereplicateReads | 0.086 | 0.002 | 0.109 | |
| doRCtest | 3.616 | 0.181 | 4.645 | |
| extractFeature | 0.231 | 0.053 | 0.370 | |
| extractSeqs | 0.888 | 0.111 | 1.300 | |
| findAndTrimSeq | 1.531 | 0.303 | 2.514 | |
| findBarcodes | 0.897 | 0.006 | 1.259 | |
| findIntegrations | 0.000 | 0.001 | 0.000 | |
| findLTRs | 0.001 | 0.001 | 0.001 | |
| findLinkers | 0.000 | 0.001 | 0.000 | |
| findPrimers | 0.000 | 0.001 | 0.001 | |
| findVector | 0.000 | 0.000 | 0.004 | |
| getIntegrationSites | 2.253 | 0.022 | 2.905 | |
| getSectorsForSamples | 0.150 | 0.004 | 0.202 | |
| getSonicAbund | 0.685 | 0.417 | 1.205 | |
| isuSites | 5.147 | 0.406 | 7.179 | |
| otuSites | 5.420 | 0.035 | 7.245 | |
| pairUpAlignments | 0.001 | 0.001 | 0.001 | |
| pairwiseAlignSeqs | 2.875 | 1.073 | 4.893 | |
| primerIDAlignSeqs | 3.71 | 0.59 | 5.48 | |
| pslCols | 0.001 | 0.001 | 0.003 | |
| pslToRangedObject | 0.439 | 0.012 | 0.586 | |
| read.BAMasPSL | 0 | 0 | 0 | |
| read.SeqFolder | 2.372 | 0.151 | 3.677 | |
| read.blast8 | 0.000 | 0.000 | 0.001 | |
| read.psl | 0.000 | 0.000 | 0.001 | |
| read.sampleInfo | 2.352 | 0.025 | 3.300 | |
| read.seqsFromSector | 0.000 | 0.001 | 0.000 | |
| removeReadsWithNs | 0.042 | 0.003 | 0.050 | |
| replicateReads | 0.098 | 0.004 | 0.131 | |
| sampleSummary | 1.575 | 0.044 | 2.154 | |
| splitByBarcode | 0.064 | 0.003 | 0.084 | |
| splitSeqsToFiles | 0.296 | 0.013 | 0.443 | |
| startgfServer | 0.001 | 0.001 | 0.000 | |
| trimSeqs | 0.056 | 0.003 | 0.083 | |
| vpairwiseAlignSeqs | 2.512 | 1.004 | 4.424 | |
| write.listedDNAStringSet | 0.000 | 0.000 | 0.001 | |
| write.psl | 0.040 | 0.008 | 0.048 | |