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This page was generated on 2025-08-04 11:43 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 465/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
crisprDesign 1.10.0  (landing page)
Jean-Philippe Fortin
Snapshot Date: 2025-07-31 13:40 -0400 (Thu, 31 Jul 2025)
git_url: https://git.bioconductor.org/packages/crisprDesign
git_branch: RELEASE_3_21
git_last_commit: 30df11a
git_last_commit_date: 2025-04-15 12:53:58 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for crisprDesign on merida1

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: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2025-08-01 01:54:33 -0400 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 02:14:13 -0400 (Fri, 01 Aug 2025)
EllapsedTime: 1179.8 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/crisprDesign.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crisprDesign/DESCRIPTION’ ... OK
* this is package ‘crisprDesign’ version ‘1.10.0’
* 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 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
addSNPAnnotation 29.309  0.257  30.227
addEditedAlleles 26.464  0.619  27.673
* 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-3.21-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-x86_64/Resources/library’
* installing *source* package ‘crisprDesign’ ...
** this is package ‘crisprDesign’ version ‘1.10.0’
** 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)

Tests output

crisprDesign.Rcheck/tests/testthat.Rout


R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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 
415.378   9.063 443.764 

Example timings

crisprDesign.Rcheck/crisprDesign-Ex.timings

nameusersystemelapsed
GuideSet-class0.2740.0100.284
GuideSet2DataFrames3.5570.2403.837
PairedGuideSet-class0.9370.0741.026
TxDb2GRangesList0.0010.0010.001
addCompositeScores2.1840.0222.231
addDistanceToTss0.0740.0030.078
addEditedAlleles26.464 0.61927.673
addExonTable0.0000.0010.002
addGeneAnnotation3.2170.1893.673
addIsoformAnnotation0.2390.0080.253
addNtcs0.7640.0400.866
addOffTargetScores0.4920.0130.546
addOnTargetScores0.0000.0000.001
addOpsBarcodes0.0520.0040.081
addPamScores1.0360.0191.109
addRepeats0.4950.0280.529
addRestrictionEnzymes1.4920.0241.528
addSNPAnnotation29.309 0.25730.227
addSequenceFeatures1.0160.0121.077
addSpacerAlignments0.0030.0010.006
addTssAnnotation0.3730.0100.417
addTxTable0.0010.0010.004
completeSpacers0.6470.1141.101
convertToMinMaxGRanges0.1060.0050.161
convertToProtospacerGRanges0.4170.0290.638
designOpsLibrary0.2160.0160.238
findSpacerPairs4.6120.1214.866
findSpacers2.9390.0583.188
getBarcodeDistanceMatrix2.0820.0722.161
getConsensusIsoform0.1500.0030.153
getMrnaSequences0.6380.0530.707
getPreMrnaSequences0.5750.0410.619
getTssObjectFromTxObject0.1430.0020.144
getTxDb0.0000.0010.001
getTxInfoDataFrame1.5480.1481.709
preparePfamTable0.0030.0020.005
queryTss0.0490.0030.053
queryTxObject0.0620.0050.068
rankSpacers3.8550.0754.011
removeRepeats0.5030.0300.538
updateOpsLibrary0.4360.0050.444
validateOpsLibrary0.3130.0050.319