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This page was generated on 2023-10-20 09:38:00 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 452/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
crisprDesign 1.2.0  (landing page)
Jean-Philippe Fortin
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/crisprDesign
git_branch: RELEASE_3_17
git_last_commit: 16ad3b4
git_last_commit_date: 2023-04-25 11:39:18 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for crisprDesign on kjohnson2


To the developers/maintainers of the crisprDesign package:
- 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: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2023-10-17 12:41:26 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 12:57:14 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 948.3 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/crisprDesign.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crisprDesign/DESCRIPTION’ ... OK
* this is package ‘crisprDesign’ version ‘1.2.0’
* 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 ... 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 ... OK
* 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 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 15.449  0.203  23.975
addEditedAlleles 12.455  0.299  19.604
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/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/4.3-arm64/Resources/library’
* installing *source* package ‘crisprDesign’ ...
** 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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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 1018 ]

══ 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 1018 ]
> 
> proc.time()
   user  system elapsed 
218.805   5.551 354.477 

Example timings

crisprDesign.Rcheck/crisprDesign-Ex.timings

nameusersystemelapsed
GuideSet-class0.1910.0040.279
GuideSet2DataFrames1.2470.0421.965
PairedGuideSet-class0.5770.0410.961
TxDb2GRangesList000
addCompositeScores1.4230.0462.260
addDistanceToTss0.8980.0111.408
addEditedAlleles12.455 0.29919.604
addExonTable0.0010.0000.001
addGeneAnnotation1.9850.1043.175
addIsoformAnnotation0.1520.0030.239
addNtcs0.4880.0210.776
addOffTargetScores0.3080.0070.485
addOnTargetScores000
addOpsBarcodes0.0430.0010.068
addPamScores0.5440.0060.859
addRepeats0.3910.0230.630
addRestrictionEnzymes0.8860.0111.372
addSNPAnnotation15.449 0.20323.975
addSequenceFeatures0.5580.0060.858
addSpacerAlignments0.0010.0000.002
addTssAnnotation0.2410.0040.380
addTxTable0.0010.0000.001
completeSpacers0.5030.0370.832
convertToMinMaxGRanges0.0720.0020.113
convertToProtospacerGRanges0.3590.0210.572
designOpsLibrary0.1510.0030.225
findSpacerPairs2.6710.0744.190
findSpacers1.9490.0483.042
getBarcodeDistanceMatrix1.4730.0282.311
getConsensusIsoform0.0960.0020.164
getMrnaSequences0.4440.0300.715
getPreMrnaSequences0.3940.0280.646
getTssObjectFromTxObject0.0730.0020.113
getTxDb0.0000.0000.001
getTxInfoDataFrame0.9900.0821.674
preparePfamTable0.0020.0010.009
queryTss0.0450.0020.069
queryTxObject0.0370.0030.060
rankSpacers2.2810.0483.627
removeRepeats0.3630.0220.578
updateOpsLibrary0.2280.0030.346
validateOpsLibrary0.2270.0040.344