Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-22 11:34 -0500 (Fri, 22 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4742 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4456 |
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 448/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
crisprBowtie 1.11.0 (landing page) Jean-Philippe Fortin
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the crisprBowtie package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/crisprBowtie.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: crisprBowtie |
Version: 1.11.0 |
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:crisprBowtie.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings crisprBowtie_1.11.0.tar.gz |
StartedAt: 2024-11-22 00:07:38 -0500 (Fri, 22 Nov 2024) |
EndedAt: 2024-11-22 00:12:03 -0500 (Fri, 22 Nov 2024) |
EllapsedTime: 265.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: crisprBowtie.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:crisprBowtie.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings crisprBowtie_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/crisprBowtie.Rcheck' * using R Under development (unstable) (2024-10-26 r87273 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'crisprBowtie/DESCRIPTION' ... OK * this is package 'crisprBowtie' version '1.11.0' * 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 ... OK * checking for portable file names ... OK * checking whether package 'crisprBowtie' 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: runCrisprBowtie.Rd: BSgenome-class, CrisprNuclease-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 files in 'vignettes' ... OK * checking examples ... OK * 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: 2 NOTEs See 'E:/biocbuild/bbs-3.21-bioc/meat/crisprBowtie.Rcheck/00check.log' for details.
crisprBowtie.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL crisprBowtie ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'crisprBowtie' ... ** using staged installation ** R ** 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 (crisprBowtie)
crisprBowtie.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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(crisprBowtie) > > test_check("crisprBowtie") # reads processed: 3 # reads with at least one alignment: 1 (33.33%) # reads that failed to align: 2 (66.67%) Reported 1 alignments # reads processed: 3 # reads with at least one alignment: 3 (100.00%) # reads that failed to align: 0 (0.00%) Reported 14 alignments # reads processed: 3 # reads with at least one alignment: 3 (100.00%) # reads that failed to align: 0 (0.00%) Reported 118 alignments # reads processed: 3 # reads with at least one alignment: 3 (100.00%) # reads that failed to align: 0 (0.00%) Reported 561 alignments # reads processed: 1 # reads with at least one alignment: 0 (0.00%) # reads that failed to align: 1 (100.00%) No alignments [runCrisprBowtie] Searching for SpCas9 protospacers # reads processed: 28 # reads with at least one alignment: 3 (10.71%) # reads that failed to align: 25 (89.29%) Reported 3 alignments [runCrisprBowtie] Searching for SpCas9 protospacers # reads processed: 28 # reads with at least one alignment: 13 (46.43%) # reads that failed to align: 15 (53.57%) Reported 13 alignments [runCrisprBowtie] Searching for SpCas9 protospacers # reads processed: 28 # reads with at least one alignment: 18 (64.29%) # reads that failed to align: 10 (35.71%) Reported 18 alignments [runCrisprBowtie] Searching for SpCas9 protospacers # reads processed: 28 # reads with at least one alignment: 25 (89.29%) # reads that failed to align: 3 (10.71%) Reported 25 alignments [runCrisprBowtie] Searching for SpCas9 protospacers # reads processed: 84 # reads with at least one alignment: 4 (4.76%) # reads that failed to align: 80 (95.24%) Reported 4 alignments [runCrisprBowtie] Searching for SpCas9 protospacers # reads processed: 84 # reads with at least one alignment: 23 (27.38%) # reads that failed to align: 61 (72.62%) Reported 23 alignments [runCrisprBowtie] Searching for SpCas9 protospacers # reads processed: 84 # reads with at least one alignment: 47 (55.95%) # reads that failed to align: 37 (44.05%) Reported 47 alignments [runCrisprBowtie] Searching for SpCas9 protospacers # reads processed: 84 # reads with at least one alignment: 61 (72.62%) # reads that failed to align: 23 (27.38%) Reported 61 alignments [runCrisprBowtie] Searching for SpCas9 protospacers [runCrisprBowtie] Searching for SpCas9 protospacers # reads processed: 84 # reads with at least one alignment: 72 (85.71%) # reads that failed to align: 12 (14.29%) Reported 72 alignments [runCrisprBowtie] Searching for AsCas12a protospacers # reads processed: 18 # reads with at least one alignment: 3 (16.67%) # reads that failed to align: 15 (83.33%) Reported 3 alignments [runCrisprBowtie] Searching for AsCas12a protospacers # reads processed: 18 # reads with at least one alignment: 10 (55.56%) # reads that failed to align: 8 (44.44%) Reported 10 alignments [runCrisprBowtie] Searching for AsCas12a protospacers # reads processed: 18 # reads with at least one alignment: 13 (72.22%) # reads that failed to align: 5 (27.78%) Reported 13 alignments [runCrisprBowtie] Searching for AsCas12a protospacers # reads processed: 18 # reads with at least one alignment: 16 (88.89%) # reads that failed to align: 2 (11.11%) Reported 16 alignments [runCrisprBowtie] Searching for AsCas12a protospacers [runCrisprBowtie] Searching for AsCas12a protospacers # reads processed: 18 # reads with at least one alignment: 16 (88.89%) # reads that failed to align: 2 (11.11%) Reported 16 alignments [ FAIL 0 | WARN 0 | SKIP 0 | PASS 21 ] > > proc.time() user system elapsed 14.04 0.84 18.07
crisprBowtie.Rcheck/crisprBowtie-Ex.timings
name | user | system | elapsed | |
runBowtie | 0.27 | 0.10 | 1.42 | |
runCrisprBowtie | 0.19 | 0.04 | 0.81 | |