Jean-Philippe Fortin
| Snapshot Date: 2025-10-31 13:40 -0400 (Fri, 31 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/crisprDesign |
| git_branch: devel |
| git_last_commit: dd162c8 |
| git_last_commit_date: 2025-10-29 11:17:54 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-01 11:32 -0400 (Sat, 01 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4774 |
| 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 463/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| crisprDesign 1.13.0 (landing page) Jean-Philippe Fortin
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the crisprDesign package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/crisprDesign.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: crisprDesign |
| Version: 1.13.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:crisprDesign.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings crisprDesign_1.13.0.tar.gz |
| StartedAt: 2025-10-31 22:21:02 -0400 (Fri, 31 Oct 2025) |
| EndedAt: 2025-10-31 22:30:46 -0400 (Fri, 31 Oct 2025) |
| EllapsedTime: 584.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: crisprDesign.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:crisprDesign.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings crisprDesign_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/crisprDesign.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘crisprDesign/DESCRIPTION’ ... OK
* this is package ‘crisprDesign’ version ‘1.13.0’
* package encoding: UTF-8
* 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 ‘crisprDesign’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... OK
* 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:
GuideSet-class.Rd: CrisprNuclease-class, BSgenome-class,
DNAStringSet-class, Seqinfo-class
PairedGuideSet-class.Rd: DNAStringSet-class
TxDb2GRangesList.Rd: TxDb-class, GRangesList-class
addCrispraiScores.Rd: GRanges-class
addEditedAlleles.Rd: BaseEditor-class
addExonTable.Rd: TxDb-class, GRangesList-class
addGeneAnnotation.Rd: TxDb-class, GRangesList-class
addNtcs.Rd: Seqinfo-class
addPamScores.Rd: CrisprNuclease-class
addPfamDomains.Rd: DataFrame-class
addRepeats.Rd: GRanges-class
addSNPAnnotation.Rd: VCF-class
addSpacerAlignments.Rd: TxDb-class, GRangesList-class, GRanges-class,
BSgenome-class, CrisprNuclease-class
addTssAnnotation.Rd: GRanges-class
addTxTable.Rd: TxDb-class, GRangesList-class
completeSpacers.Rd: CrisprNuclease-class, BSgenome-class
designCompleteAnnotation.Rd: BSgenome-class, GRanges-class,
VCF-class, CrisprNuclease-class, TxDb-class, GRangesList-class,
DataFrame-class
findSpacerPairs.Rd: GRanges-class, DNAStringSet-class,
DNAString-class, CrisprNuclease-class, BSgenome-class
findSpacers.Rd: GRanges-class, DNAStringSet-class, DNAString-class,
CrisprNuclease-class, BSgenome-class
getConsensusIsoform.Rd: TxDb-class, GRangesList-class
getMrnaSequences.Rd: TxDb-class, GRangesList-class, BSgenome-class,
DNAStringSet-class
getPreMrnaSequences.Rd: TxDb-class, GRangesList-class,
BSgenome-class, DNAStringSet-class
getTssObjectFromTxObject.Rd: TxDb-class, GRangesList-class
getTxDb.Rd: TxDb-class, makeTxDbFromGFF, makeTxDbFromEnsembl
getTxInfoDataFrame.Rd: TxDb-class, GRangesList-class, BSgenome-class,
GRanges-class
grListExample.Rd: TxDb-class, GRangesList-class
grRepeatsExample.Rd: GRanges-class
preparePfamTable.Rd: TxDb-class, GRangesList-class, DataFrame-class
queryTss.Rd: GRanges-class
queryTxObject.Rd: TxDb-class, GRangesList-class, GRanges-class
removeRepeats.Rd: GRanges-class
tssObjectExample.Rd: GRanges-class
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 LazyData ... 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
addEditedAlleles 11.510 0.483 11.995
addSNPAnnotation 10.924 0.028 10.952
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
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-3.23-bioc/meat/crisprDesign.Rcheck/00check.log’
for details.
crisprDesign.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL crisprDesign ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘crisprDesign’ ... ** this is package ‘crisprDesign’ version ‘1.13.0’ ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (crisprDesign)
crisprDesign.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(crisprDesign)
Loading required package: crisprBase
>
> test_check("crisprDesign")
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38
[runCrisprBowtie] Searching for SpCas9 protospacers
# reads processed: 7
# reads with at least one alignment: 6 (85.71%)
# reads that failed to align: 1 (14.29%)
Reported 6 alignments
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38
[runCrisprBowtie] Searching for SpCas9 protospacers
# reads processed: 7
# reads with at least one alignment: 6 (85.71%)
# reads that failed to align: 1 (14.29%)
Reported 6 alignments
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38
[runCrisprBowtie] Searching for SpCas9 protospacers
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38
[runCrisprBowtie] Searching for SpCas9 protospacers
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38
[runCrisprBowtie] Searching for SpCas9 protospacers
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38
[runCrisprBowtie] Searching for SpCas9 protospacers
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38
[runCrisprBowtie] Searching for SpCas9 protospacers
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38
[runCrisprBowtie] Searching for SpCas9 protospacers
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38
[runCrisprBowtie] Searching for SpCas9 protospacers
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38
[runCrisprBowtie] Searching for SpCas9 protospacers
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38
[runCrisprBowtie] Searching for SpCas9 protospacers
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
[runCrisprBowtie] Using BSgenome.Hsapiens.UCSC.hg38
[runCrisprBowtie] Searching for SpCas9 protospacers
# reads processed: 6
# reads with at least one alignment: 6 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 6 alignments
[ FAIL 0 | WARN 0 | SKIP 78 | PASS 1090 ]
══ Skipped tests (78) ══════════════════════════════════════════════════════════
• empty test (69): 'test-GuideSet-class.R:214:1',
'test-GuideSet-class.R:225:1', 'test-GuideSet-class.R:230:1',
'test-addGeneAnnotation.R:17:1', 'test-addGeneAnnotation.R:116:1',
'test-addGeneAnnotation.R:174:1', 'test-addNtcs.R:352:1',
'test-addNtcs.R:398:1', 'test-addOffTargetScores.R:21:1',
'test-addOnTargetScores.R:20:1', 'test-addOnTargetScores.R:67:1',
'test-addOnTargetScores.R:87:1', 'test-addOnTargetScores.R:101:1',
'test-addOnTargetScores.R:145:1', 'test-addOnTargetScores.R:157:1',
'test-addOnTargetScores.R:190:1', 'test-addPamScores.R:30:1',
'test-addRepeats.R:78:1', 'test-addRepeats.R:84:1', 'test-addRepeats.R:89:1',
'test-addRestrictionEnzymes.R:89:1', 'test-addRestrictionEnzymes.R:180:1',
'test-addRestrictionEnzymes.R:185:1', 'test-addRestrictionEnzymes.R:191:1',
'test-addRestrictionEnzymes.R:198:1', 'test-addSpacerAlignments.R:63:1',
'test-addSpacerAlignments.R:147:1', 'test-addSpacerAlignments.R:199:1',
'test-addSpacerAlignments.R:266:1', 'test-addSpacerAlignments.R:349:1',
'test-addSpacerAlignments.R:469:1', 'test-addSpacerAlignments.R:509:1',
'test-addSpacerAlignments.R:546:1', 'test-addSpacerAlignments.R:572:1',
'test-addSpacerAlignments.R:603:1', 'test-addSpacerAlignments.R:627:1',
'test-addSpacerAlignments.R:650:1', 'test-addSpacerAlignments.R:669:1',
'test-addSpacerAlignments.R:720:1', 'test-completeSpacers.R:27:1',
'test-completeSpacers.R:32:1', 'test-completeSpacers.R:37:1',
'test-completeSpacers.R:42:1', 'test-completeSpacers.R:47:1',
'test-completeSpacers.R:52:1', 'test-completeSpacers.R:60:1',
'test-completeSpacers.R:73:1', 'test-completeSpacers.R:78:1',
'test-completeSpacers.R:83:1', 'test-completeSpacers.R:88:1',
'test-completeSpacers.R:93:1', 'test-completeSpacers.R:113:1',
'test-completeSpacers.R:118:1', 'test-completeSpacers.R:123:1',
'test-completeSpacers.R:128:1', 'test-completeSpacers.R:133:1',
'test-completeSpacers.R:139:1', 'test-completeSpacers.R:144:1',
'test-completeSpacers.R:167:1', 'test-completeSpacers.R:172:1',
'test-completeSpacers.R:177:1', 'test-completeSpacers.R:182:1',
'test-completeSpacers.R:187:1', 'test-completeSpacers.R:193:1',
'test-completeSpacers.R:198:1', 'test-completeSpacers.R:203:1',
'test-completeSpacers.R:208:1', 'test-completeSpacers.R:213:1',
'test-queryTxObject.R:152:1'
• long run time (8): 'test-TxDb2GRangesList.R:19:5',
'test-TxDb2GRangesList.R:36:5', 'test-TxDb2GRangesList.R:56:5',
'test-TxDb2GRangesList.R:77:5', 'test-addSNPAnnotation.R:33:5',
'test-addSNPAnnotation.R:70:5', 'test-addSNPAnnotation.R:79:5',
'test-addSNPAnnotation.R:124:5'
• no del for guideSetExample (1): 'test-addSNPAnnotation.R:148:5'
[ FAIL 0 | WARN 0 | SKIP 78 | PASS 1090 ]
>
> proc.time()
user system elapsed
170.665 5.733 176.615
crisprDesign.Rcheck/crisprDesign-Ex.timings
| name | user | system | elapsed | |
| GuideSet-class | 0.128 | 0.008 | 0.136 | |
| GuideSet2DataFrames | 1.344 | 0.075 | 1.420 | |
| PairedGuideSet-class | 0.374 | 0.042 | 0.416 | |
| TxDb2GRangesList | 0 | 0 | 0 | |
| addCompositeScores | 0.942 | 0.083 | 1.026 | |
| addDistanceToTss | 0.032 | 0.002 | 0.035 | |
| addEditedAlleles | 11.510 | 0.483 | 11.995 | |
| addExonTable | 0 | 0 | 0 | |
| addGeneAnnotation | 1.305 | 0.023 | 1.328 | |
| addIsoformAnnotation | 0.097 | 0.000 | 0.098 | |
| addNtcs | 0.291 | 0.004 | 0.296 | |
| addOffTargetScores | 0.227 | 0.003 | 0.230 | |
| addOnTargetScores | 0.000 | 0.000 | 0.001 | |
| addOpsBarcodes | 0.028 | 0.003 | 0.031 | |
| addPamScores | 0.383 | 0.001 | 0.384 | |
| addRepeats | 0.196 | 0.011 | 0.209 | |
| addRestrictionEnzymes | 0.646 | 0.011 | 0.657 | |
| addSNPAnnotation | 10.924 | 0.028 | 10.952 | |
| addSequenceFeatures | 0.431 | 0.005 | 0.436 | |
| addSpacerAlignments | 0.001 | 0.000 | 0.001 | |
| addTssAnnotation | 0.159 | 0.000 | 0.159 | |
| addTxTable | 0 | 0 | 0 | |
| completeSpacers | 0.341 | 0.037 | 0.378 | |
| convertToMinMaxGRanges | 0.057 | 0.001 | 0.058 | |
| convertToProtospacerGRanges | 0.226 | 0.003 | 0.228 | |
| designOpsLibrary | 0.107 | 0.000 | 0.107 | |
| findSpacerPairs | 1.866 | 0.052 | 1.918 | |
| findSpacers | 1.240 | 0.042 | 1.282 | |
| getBarcodeDistanceMatrix | 1.460 | 0.068 | 1.528 | |
| getConsensusIsoform | 0.061 | 0.002 | 0.062 | |
| getMrnaSequences | 0.286 | 0.014 | 0.301 | |
| getPreMrnaSequences | 0.268 | 0.014 | 0.282 | |
| getTssObjectFromTxObject | 0.059 | 0.001 | 0.060 | |
| getTxDb | 0 | 0 | 0 | |
| getTxInfoDataFrame | 0.670 | 0.077 | 0.747 | |
| preparePfamTable | 0.001 | 0.000 | 0.002 | |
| queryTss | 0.021 | 0.000 | 0.021 | |
| queryTxObject | 0.025 | 0.002 | 0.028 | |
| rankSpacers | 1.525 | 0.008 | 1.534 | |
| removeRepeats | 0.225 | 0.003 | 0.227 | |
| updateOpsLibrary | 0.168 | 0.002 | 0.169 | |
| validateOpsLibrary | 0.148 | 0.000 | 0.148 | |