| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-27 05:50:32 -0000 (Mon, 27 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6083 |
| 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 | ||||
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To the developers/maintainers of the crisprDesign package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 445/2195 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| crisprDesign 1.1.24 (landing page) Jean-Philippe Fortin
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: crisprDesign |
| Version: 1.1.24 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:crisprDesign.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings crisprDesign_1.1.24.tar.gz |
| StartedAt: 2023-03-25 00:12:30 -0000 (Sat, 25 Mar 2023) |
| EndedAt: 2023-03-25 00:24:41 -0000 (Sat, 25 Mar 2023) |
| EllapsedTime: 730.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: crisprDesign.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:crisprDesign.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings crisprDesign_1.1.24.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/crisprDesign.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘crisprDesign/DESCRIPTION’ ... OK
* this is package ‘crisprDesign’ version ‘1.1.24’
* 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 16.189 0.156 16.356
addEditedAlleles 14.037 0.280 14.320
* 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 ...
‘intro.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/crisprDesign.Rcheck/00check.log’
for details.
crisprDesign.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL crisprDesign ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-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 Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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 ═══════════════════════════════════════════════════════════════
• empty test (69)
• long run time (8)
• no del for guideSetExample (1)
[ FAIL 0 | WARN 0 | SKIP 78 | PASS 1018 ]
>
> proc.time()
user system elapsed
231.612 6.943 241.355
crisprDesign.Rcheck/crisprDesign-Ex.timings
| name | user | system | elapsed | |
| GuideSet-class | 0.175 | 0.000 | 0.179 | |
| GuideSet2DataFrames | 1.176 | 0.052 | 1.465 | |
| PairedGuideSet-class | 0.586 | 0.048 | 0.634 | |
| TxDb2GRangesList | 0.001 | 0.000 | 0.000 | |
| addCompositeScores | 2.337 | 0.300 | 2.640 | |
| addDistanceToTss | 0.048 | 0.000 | 0.048 | |
| addEditedAlleles | 14.037 | 0.280 | 14.320 | |
| addExonTable | 0 | 0 | 0 | |
| addGeneAnnotation | 1.880 | 0.040 | 1.978 | |
| addIsoformAnnotation | 0.181 | 0.000 | 0.181 | |
| addNtcs | 0.400 | 0.016 | 0.416 | |
| addOffTargetScores | 0.362 | 0.004 | 0.366 | |
| addOnTargetScores | 0.000 | 0.000 | 0.001 | |
| addOpsBarcodes | 0.042 | 0.004 | 0.046 | |
| addPamScores | 0.672 | 0.004 | 0.676 | |
| addRepeats | 0.289 | 0.000 | 0.289 | |
| addRestrictionEnzymes | 0.937 | 0.012 | 0.949 | |
| addSNPAnnotation | 16.189 | 0.156 | 16.356 | |
| addSequenceFeatures | 0.581 | 0.004 | 0.585 | |
| addSpacerAlignments | 0.001 | 0.000 | 0.001 | |
| addTssAnnotation | 0.271 | 0.000 | 0.273 | |
| addTxTable | 0.000 | 0.001 | 0.000 | |
| completeSpacers | 0.435 | 0.015 | 0.450 | |
| convertToMinMaxGRanges | 0.077 | 0.000 | 0.076 | |
| convertToProtospacerGRanges | 0.267 | 0.008 | 0.275 | |
| designOpsLibrary | 0.145 | 0.000 | 0.148 | |
| findSpacerPairs | 2.675 | 0.048 | 2.725 | |
| findSpacers | 1.787 | 0.011 | 1.804 | |
| getBarcodeDistanceMatrix | 1.267 | 0.059 | 1.333 | |
| getConsensusIsoform | 0.092 | 0.000 | 0.094 | |
| getMrnaSequences | 0.339 | 0.035 | 0.575 | |
| getPreMrnaSequences | 0.294 | 0.017 | 0.310 | |
| getTssObjectFromTxObject | 0.064 | 0.004 | 0.067 | |
| getTxDb | 0.001 | 0.000 | 0.000 | |
| getTxInfoDataFrame | 1.844 | 0.831 | 3.332 | |
| preparePfamTable | 0.000 | 0.002 | 0.005 | |
| queryTss | 0.046 | 0.001 | 0.046 | |
| queryTxObject | 0.030 | 0.008 | 0.039 | |
| rankSpacers | 2.318 | 0.024 | 2.351 | |
| removeRepeats | 0.272 | 0.000 | 0.272 | |
| updateOpsLibrary | 0.218 | 0.000 | 0.219 | |
| validateOpsLibrary | 0.181 | 0.000 | 0.181 | |