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This page was generated on 2025-08-09 12:09 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 462/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
crisprDesign 1.11.1  (landing page)
Jean-Philippe Fortin
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/crisprDesign
git_branch: devel
git_last_commit: eb7b7de
git_last_commit_date: 2025-07-17 20:07:40 -0400 (Thu, 17 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows 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
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for crisprDesign on kjohnson3

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.

raw results


Summary

Package: crisprDesign
Version: 1.11.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:crisprDesign.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings crisprDesign_1.11.1.tar.gz
StartedAt: 2025-08-08 18:50:06 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 18:53:27 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 201.3 seconds
RetCode: 0
Status:   OK  
CheckDir: crisprDesign.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:crisprDesign.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings crisprDesign_1.11.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/crisprDesign.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crisprDesign/DESCRIPTION’ ... OK
* this is package ‘crisprDesign’ version ‘1.11.1’
* 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 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
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/crisprDesign.Rcheck/00check.log’
for details.


Installation output

crisprDesign.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL crisprDesign
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘crisprDesign’ ...
** this is package ‘crisprDesign’ version ‘1.11.1’
** 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)

Tests output

crisprDesign.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 
 58.298   1.779  61.206 

Example timings

crisprDesign.Rcheck/crisprDesign-Ex.timings

nameusersystemelapsed
GuideSet-class0.0440.0010.045
GuideSet2DataFrames0.4490.0220.470
PairedGuideSet-class0.1380.0140.152
TxDb2GRangesList000
addCompositeScores0.3200.0060.325
addDistanceToTss0.0140.0010.015
addEditedAlleles4.7070.1734.882
addExonTable000
addGeneAnnotation0.4470.0200.467
addIsoformAnnotation0.0360.0010.037
addNtcs0.1110.0090.122
addOffTargetScores0.0770.0020.079
addOnTargetScores000
addOpsBarcodes0.0130.0010.013
addPamScores0.1180.0000.118
addRepeats0.0830.0070.089
addRestrictionEnzymes0.2270.0050.232
addSNPAnnotation3.4050.0213.432
addSequenceFeatures0.1220.0000.122
addSpacerAlignments0.0010.0000.001
addTssAnnotation0.0520.0010.055
addTxTable0.0010.0000.001
completeSpacers0.1190.0110.130
convertToMinMaxGRanges0.0200.0000.021
convertToProtospacerGRanges0.0870.0080.094
designOpsLibrary0.0370.0020.038
findSpacerPairs0.6330.0250.665
findSpacers0.4000.0160.417
getBarcodeDistanceMatrix0.4440.0110.456
getConsensusIsoform0.0200.0010.021
getMrnaSequences0.1040.0120.115
getPreMrnaSequences0.0950.0100.104
getTssObjectFromTxObject0.0180.0000.018
getTxDb0.0000.0000.001
getTxInfoDataFrame0.2380.0320.270
preparePfamTable0.0010.0000.000
queryTss0.0070.0000.007
queryTxObject0.0080.0010.009
rankSpacers0.4920.0130.505
removeRepeats0.0820.0090.093
updateOpsLibrary0.0520.0010.053
validateOpsLibrary0.0470.0010.049