Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:31 -0500 (Mon, 02 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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 GenomeInfoDb package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 766/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomeInfoDb 1.35.9 (landing page) Hervé Pagès
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | ||||||||
Package: GenomeInfoDb |
Version: 1.35.9 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomeInfoDb.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GenomeInfoDb_1.35.9.tar.gz |
StartedAt: 2022-12-29 00:03:49 -0500 (Thu, 29 Dec 2022) |
EndedAt: 2022-12-29 00:06:13 -0500 (Thu, 29 Dec 2022) |
EllapsedTime: 143.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: GenomeInfoDb.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomeInfoDb.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GenomeInfoDb_1.35.9.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/GenomeInfoDb.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 'GenomeInfoDb/DESCRIPTION' ... OK * this is package 'GenomeInfoDb' version '1.35.9' * 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 'GenomeInfoDb' 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 ... NOTE Unexported object imported by a ':::' call: 'utils:::.roman2numeric' See the note in ?`:::` about the use of this operator. * 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 ... WARNING checkRd: (5) GenomeDescription-class.Rd:53-58: \item in \describe must have non-empty label checkRd: (5) GenomeDescription-class.Rd:59-63: \item in \describe must have non-empty label checkRd: (5) GenomeDescription-class.Rd:64-70: \item in \describe must have non-empty label checkRd: (5) GenomeDescription-class.Rd:71-75: \item in \describe must have non-empty label checkRd: (5) GenomeDescription-class.Rd:76-79: \item in \describe must have non-empty label checkRd: (5) GenomeDescription-class.Rd:80-88: \item in \describe must have non-empty label checkRd: (5) Seqinfo-class.Rd:83-93: \item in \describe must have non-empty label checkRd: (5) Seqinfo-class.Rd:101-104: \item in \describe must have non-empty label checkRd: (5) Seqinfo-class.Rd:105-115: \item in \describe must have non-empty label checkRd: (5) Seqinfo-class.Rd:116-119: \item in \describe must have non-empty label checkRd: (5) Seqinfo-class.Rd:120-123: \item in \describe must have non-empty label checkRd: (5) Seqinfo-class.Rd:124-149: \item in \describe must have non-empty label checkRd: (5) Seqinfo-class.Rd:150-153: \item in \describe must have non-empty label checkRd: (5) Seqinfo-class.Rd:154-157: \item in \describe must have non-empty label checkRd: (5) Seqinfo-class.Rd:158-162: \item in \describe must have non-empty label checkRd: (5) Seqinfo-class.Rd:170-178: \item in \describe must have non-empty label checkRd: (5) Seqinfo-class.Rd:186-189: \item in \describe must have non-empty label checkRd: (5) Seqinfo-class.Rd:226-249: \item in \describe must have non-empty label checkRd: (5) Seqinfo-class.Rd:250-256: \item in \describe must have non-empty label checkRd: (5) Seqinfo-class.Rd:257-262: \item in \describe must have non-empty label * 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 sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed loadTaxonomyDb 6.81 0.16 7.09 GenomeDescription-class 5.50 0.23 5.75 getChromInfoFromEnsembl 0.39 0.13 28.18 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'run_unitTests.R' ERROR Running the tests in 'tests/run_unitTests.R' failed. Last 13 lines of output: 1 Test Suite : GenomeInfoDb RUnit Tests - 21 test functions, 1 error, 0 failures ERROR in test_seqlevelsStyle_Seqinfo: Error in .format_NCBI_chrom_info(assembly_report, circ_seqs = circ_seqs) : is_primary_key(sequence_name) is not TRUE Test files with failing tests test_seqlevelsStyle.R test_seqlevelsStyle_Seqinfo Error in BiocGenerics:::testPackage("GenomeInfoDb") : unit tests failed for package GenomeInfoDb Calls: <Anonymous> -> <Anonymous> 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, 1 WARNING, 1 NOTE See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/GenomeInfoDb.Rcheck/00check.log' for details.
GenomeInfoDb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL GenomeInfoDb ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'GenomeInfoDb' ... ** 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 (GenomeInfoDb)
GenomeInfoDb.Rcheck/tests/run_unitTests.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. > require("GenomeInfoDb") || stop("unable to load GenomeInfoDb package") Loading required package: GenomeInfoDb Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows [1] TRUE > GenomeInfoDb:::.test() Timing stopped at: 15.03 1.49 20.05 Error in .format_NCBI_chrom_info(assembly_report, circ_seqs = circ_seqs) : is_primary_key(sequence_name) is not TRUE In addition: Warning messages: 1: In (function (seqlevels, genome, new_style) : cannot switch some of apiMel2's seqlevels from UCSC to NCBI style 2: In (function (seqlevels, genome, new_style) : cannot switch some of Amel_2.0's seqlevels from NCBI to UCSC style 3: In (function (seqlevels, genome, new_style) : cannot switch some of bosTau7's seqlevels from UCSC to NCBI style 4: In (function (seqlevels, genome, new_style) : cannot switch some of Btau_4.6.1's seqlevels from NCBI to UCSC style 5: In getChromInfoFromNCBI(genome, as.Seqinfo = TRUE) : Assembly Bos_taurus_UMD_3.1.1 is mapped to more than one assembly (GCF_000003055.5, GCA_000003055.5). The first one was selected. 6: In (function (seqlevels, genome, new_style) : cannot switch some of ARS-UCD1.2's seqlevels from NCBI to UCSC style RUNIT TEST PROTOCOL -- Thu Dec 29 00:06:04 2022 *********************************************** Number of test functions: 21 Number of errors: 1 Number of failures: 0 1 Test Suite : GenomeInfoDb RUnit Tests - 21 test functions, 1 error, 0 failures ERROR in test_seqlevelsStyle_Seqinfo: Error in .format_NCBI_chrom_info(assembly_report, circ_seqs = circ_seqs) : is_primary_key(sequence_name) is not TRUE Test files with failing tests test_seqlevelsStyle.R test_seqlevelsStyle_Seqinfo Error in BiocGenerics:::testPackage("GenomeInfoDb") : unit tests failed for package GenomeInfoDb Calls: <Anonymous> -> <Anonymous> Execution halted
GenomeInfoDb.Rcheck/GenomeInfoDb-Ex.timings
name | user | system | elapsed | |
GenomeDescription-class | 5.50 | 0.23 | 5.75 | |
NCBI-utils | 0.01 | 0.02 | 0.16 | |
Seqinfo-class | 0.23 | 0.04 | 0.36 | |
getChromInfoFromEnsembl | 0.39 | 0.13 | 28.18 | |
getChromInfoFromNCBI | 0.24 | 0.03 | 0.67 | |
getChromInfoFromUCSC | 1.79 | 1.03 | 3.92 | |
loadTaxonomyDb | 6.81 | 0.16 | 7.09 | |
mapGenomeBuilds | 0.05 | 0.00 | 0.05 | |
rankSeqlevels | 0.06 | 0.02 | 0.16 | |
seqinfo | 3.78 | 0.31 | 4.14 | |
seqlevels-wrappers | 2.58 | 0.22 | 2.81 | |
seqlevelsStyle | 2.91 | 0.44 | 4.39 | |