| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-29 11:36:40 -0400 (Fri, 29 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
| 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 456/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| crisprDesign 1.4.0 (landing page) Jean-Philippe Fortin
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.4.0 |
| Command: set _R_CHECK_FORCE_SUGGESTS_=0&& F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:crisprDesign.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings crisprDesign_1.4.0.tar.gz |
| StartedAt: 2024-03-27 23:47:18 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 23:57:29 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 610.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: crisprDesign.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### set _R_CHECK_FORCE_SUGGESTS_=0&& F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:crisprDesign.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings crisprDesign_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/crisprDesign.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.3.0
GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'crisprDesign/DESCRIPTION' ... OK
* this is package 'crisprDesign' version '1.4.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages suggested but not available for checking: 'crisprBwa', 'Rbwa'
* 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 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 12.22 0.09 12.34
addEditedAlleles 11.91 0.33 12.23
* 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: 2 NOTEs
See
'F:/biocbuild/bbs-3.18-bioc/meat/crisprDesign.Rcheck/00check.log'
for details.
crisprDesign.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL crisprDesign ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.18-bioc/R/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)
crisprDesign.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
Failed with error: 'there is no package called 'crisprBwa''
[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
Failed with error: 'there is no package called 'crisprBwa''
[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
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
[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
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
[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
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
[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
Failed with error: 'there is no package called 'crisprBwa''
[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
Failed with error: 'there is no package called 'crisprBwa''
[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
Failed with error: 'there is no package called 'crisprBwa''
[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
Failed with error: 'there is no package called 'crisprBwa''
Failed with error: 'there is no package called 'crisprBwa''
[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
Failed with error: 'there is no package called 'crisprBwa''
[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
Failed with error: 'there is no package called 'crisprBwa''
[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
Failed with error: 'there is no package called 'crisprBwa''
[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
202.87 6.60 219.34
crisprDesign.Rcheck/crisprDesign-Ex.timings
| name | user | system | elapsed | |
| GuideSet-class | 0.14 | 0.00 | 0.14 | |
| GuideSet2DataFrames | 1.20 | 0.08 | 1.28 | |
| PairedGuideSet-class | 1.48 | 0.04 | 1.53 | |
| TxDb2GRangesList | 0 | 0 | 0 | |
| addCompositeScores | 1.23 | 0.09 | 1.33 | |
| addDistanceToTss | 0.05 | 0.00 | 0.05 | |
| addEditedAlleles | 11.91 | 0.33 | 12.23 | |
| addExonTable | 0 | 0 | 0 | |
| addGeneAnnotation | 1.51 | 0.09 | 1.61 | |
| addIsoformAnnotation | 0.16 | 0.00 | 0.15 | |
| addNtcs | 0.41 | 0.05 | 0.45 | |
| addOffTargetScores | 0.3 | 0.0 | 0.3 | |
| addOnTargetScores | 0 | 0 | 0 | |
| addOpsBarcodes | 0.04 | 0.00 | 0.04 | |
| addPamScores | 0.54 | 0.03 | 0.56 | |
| addRepeats | 0.20 | 0.05 | 0.25 | |
| addRestrictionEnzymes | 0.77 | 0.00 | 0.77 | |
| addSNPAnnotation | 12.22 | 0.09 | 12.34 | |
| addSequenceFeatures | 0.37 | 0.00 | 0.37 | |
| addSpacerAlignments | 0 | 0 | 0 | |
| addTssAnnotation | 0.18 | 0.00 | 0.17 | |
| addTxTable | 0 | 0 | 0 | |
| completeSpacers | 0.39 | 0.05 | 0.44 | |
| convertToMinMaxGRanges | 0.04 | 0.00 | 0.04 | |
| convertToProtospacerGRanges | 0.25 | 0.05 | 0.30 | |
| designOpsLibrary | 0.11 | 0.00 | 0.11 | |
| findSpacerPairs | 1.91 | 0.11 | 2.01 | |
| findSpacers | 1.34 | 0.01 | 1.36 | |
| getBarcodeDistanceMatrix | 1.49 | 0.02 | 1.50 | |
| getConsensusIsoform | 0.06 | 0.00 | 0.07 | |
| getMrnaSequences | 0.27 | 0.08 | 0.34 | |
| getPreMrnaSequences | 0.42 | 0.03 | 0.45 | |
| getTssObjectFromTxObject | 0.04 | 0.00 | 0.05 | |
| getTxDb | 0 | 0 | 0 | |
| getTxInfoDataFrame | 0.74 | 0.12 | 0.86 | |
| preparePfamTable | 0 | 0 | 0 | |
| queryTss | 0.03 | 0.00 | 0.03 | |
| queryTxObject | 0.03 | 0.00 | 0.03 | |
| rankSpacers | 1.52 | 0.08 | 1.60 | |
| removeRepeats | 0.20 | 0.05 | 0.25 | |
| updateOpsLibrary | 0.18 | 0.00 | 0.19 | |
| validateOpsLibrary | 0.16 | 0.03 | 0.19 | |