| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:25 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 | ||||
|
To the developers/maintainers of the crisprDesign package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 428/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| crisprDesign 1.1.8 (landing page) Jean-Philippe Fortin
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | ||||||||
| Package: crisprDesign |
| Version: 1.1.8 |
| Command: set _R_CHECK_FORCE_SUGGESTS_=0&& F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:crisprDesign.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings crisprDesign_1.1.8.tar.gz |
| StartedAt: 2022-12-28 22:51:57 -0500 (Wed, 28 Dec 2022) |
| EndedAt: 2022-12-28 22:59:03 -0500 (Wed, 28 Dec 2022) |
| EllapsedTime: 425.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: crisprDesign.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### set _R_CHECK_FORCE_SUGGESTS_=0&& F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:crisprDesign.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings crisprDesign_1.1.8.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/crisprDesign.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'crisprDesign/DESCRIPTION' ... OK
* this is package 'crisprDesign' version '1.1.8'
* 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
addEditedAlleles 8.85 0.25 9.11
addSNPAnnotation 8.57 0.09 8.75
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
• long run time (8)
• no del for guideSetExample (1)
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-addNtcs.R:146'): (code run outside of `test_that()`) ───────────
<packageNotFoundError/error/condition>
Error in `find.package(package, lib.loc, verbose = verbose)`: there is no package called 'crisprDesignData'
Backtrace:
▆
1. └─utils::data("txdb_human", package = "crisprDesignData") at test-addNtcs.R:146:0
2. └─base::find.package(package, lib.loc, verbose = verbose)
[ FAIL 1 | WARN 0 | SKIP 76 | PASS 968 ]
Error: Test failures
Execution halted
* 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 ERROR, 2 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/crisprDesign.Rcheck/00check.log'
for details.
crisprDesign.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL crisprDesign ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-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.fail
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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''
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 1 | WARN 0 | SKIP 76 | PASS 968 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (67)
• long run time (8)
• no del for guideSetExample (1)
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-addNtcs.R:146'): (code run outside of `test_that()`) ───────────
<packageNotFoundError/error/condition>
Error in `find.package(package, lib.loc, verbose = verbose)`: there is no package called 'crisprDesignData'
Backtrace:
▆
1. └─utils::data("txdb_human", package = "crisprDesignData") at test-addNtcs.R:146:0
2. └─base::find.package(package, lib.loc, verbose = verbose)
[ FAIL 1 | WARN 0 | SKIP 76 | PASS 968 ]
Error: Test failures
Execution halted
crisprDesign.Rcheck/crisprDesign-Ex.timings
| name | user | system | elapsed | |
| GuideSet-class | 0.12 | 0.02 | 0.14 | |
| PairedGuideSet-class | 0.35 | 0.04 | 0.44 | |
| TxDb2GRangesList | 0 | 0 | 0 | |
| addCompositeScores | 0.92 | 0.05 | 0.97 | |
| addDistanceToTss | 0.04 | 0.01 | 0.05 | |
| addEditedAlleles | 8.85 | 0.25 | 9.11 | |
| addExonTable | 1.28 | 0.10 | 2.00 | |
| addGeneAnnotation | 0.97 | 0.05 | 1.01 | |
| addIsoformAnnotation | 0.11 | 0.00 | 0.11 | |
| addNtcs | 0.25 | 0.01 | 0.26 | |
| addOffTargetScores | 0.25 | 0.00 | 0.25 | |
| addOnTargetScores | 0 | 0 | 0 | |
| addOpsBarcodes | 0.01 | 0.00 | 0.02 | |
| addPamScores | 0.31 | 0.02 | 0.33 | |
| addRepeats | 0.19 | 0.01 | 0.20 | |
| addRestrictionEnzymes | 0.56 | 0.02 | 0.58 | |
| addSNPAnnotation | 8.57 | 0.09 | 8.75 | |
| addSequenceFeatures | 0.35 | 0.00 | 0.35 | |
| addSpacerAlignments | 0.01 | 0.00 | 0.01 | |
| addTssAnnotation | 0.13 | 0.00 | 0.13 | |
| addTxTable | 1.09 | 0.06 | 1.15 | |
| completeSpacers | 0.25 | 0.05 | 0.30 | |
| convertToMinMaxGRanges | 0.05 | 0.00 | 0.04 | |
| convertToProtospacerGRanges | 0.14 | 0.05 | 0.21 | |
| designOpsLibrary | 0.09 | 0.00 | 0.09 | |
| findSpacerPairs | 1.64 | 0.12 | 1.78 | |
| findSpacers | 1.11 | 0.02 | 1.12 | |
| flattenGuideSet | 0.61 | 0.01 | 0.63 | |
| getBarcodeDistanceMatrix | 2.12 | 0.02 | 2.14 | |
| getConsensusIsoform | 0.05 | 0.00 | 0.04 | |
| getMrnaSequences | 0.20 | 0.05 | 0.25 | |
| getTssObjectFromTxObject | 0.03 | 0.00 | 0.03 | |
| getTxDb | 0 | 0 | 0 | |
| getTxInfoDataFrame | 0.48 | 0.09 | 0.58 | |
| preparePfamTable | 0 | 0 | 0 | |
| queryTss | 0.03 | 0.00 | 0.03 | |
| queryTxObject | 0.02 | 0.00 | 0.02 | |
| rankSpacers | 1.30 | 0.08 | 1.37 | |
| removeRepeats | 0.14 | 0.05 | 0.19 | |
| updateOpsLibrary | 0.13 | 0.00 | 0.13 | |
| validateOpsLibrary | 0.12 | 0.00 | 0.12 | |