Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-09 17:39 -0400 (Tue, 09 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4709 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
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 850/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GEOquery 2.72.0 (landing page) Sean Davis
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the GEOquery package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GEOquery.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: GEOquery |
Version: 2.72.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GEOquery.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GEOquery_2.72.0.tar.gz |
StartedAt: 2024-07-07 23:36:58 -0400 (Sun, 07 Jul 2024) |
EndedAt: 2024-07-07 23:41:55 -0400 (Sun, 07 Jul 2024) |
EllapsedTime: 296.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: GEOquery.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GEOquery.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GEOquery_2.72.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GEOquery.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘GEOquery/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GEOquery’ version ‘2.72.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘GEOquery’ can be installed ... OK * checking installed package size ... NOTE installed size is 13.2Mb sub-directories of 1Mb or more: extdata 12.8Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License components which are templates and need '+ file LICENSE': MIT * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 ... NOTE Warning: no function found corresponding to methods exports from ‘GEOquery’ for: ‘show’ A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘R.utils’ All declared Imports should be used. Package in Depends field not imported from: ‘methods’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File ‘GEOquery/R/zzz.R’: .onLoad calls: packageStartupMessage("Setting options('download.file.method.GEOquery'='auto')") packageStartupMessage("Setting options('GEOquery.inmemory.gpl'=FALSE)") See section ‘Good practice’ in '?.onAttach'. .parseGPLTxt: no visible global function definition for ‘new’ .parseGPLWithLimits: no visible global function definition for ‘new’ .parseGSMTxt: no visible global function definition for ‘new’ .parseGSMWithLimits: no visible global function definition for ‘new’ GDS2MA: no visible global function definition for ‘new’ GDS2MA: no visible binding for global variable ‘MA’ GDS2eSet: no visible global function definition for ‘new’ fastTabRead: no visible global function definition for ‘read.table’ fastTabRead: no visible global function definition for ‘read.delim’ parseGDS: no visible global function definition for ‘new’ parseGSE: no visible global function definition for ‘new’ parseGSEMatrix: no visible global function definition for ‘new’ parseGSEMatrix: no visible binding for global variable ‘.’ parseGSEMatrix: no visible binding for global variable ‘characteristics’ parseGSEMatrix: no visible binding for global variable ‘kvpair’ parseGSEMatrix: no visible binding for global variable ‘accession’ parseGSEMatrix: no visible binding for global variable ‘k’ parseGSEMatrix: no visible binding for global variable ‘v’ parseGSEMatrix: no visible global function definition for ‘read.table’ parseGSEMatrix: no visible global function definition for ‘as’ Undefined global functions or variables: . MA accession as characteristics k kvpair new read.delim read.table v Consider adding importFrom("methods", "as", "new") importFrom("utils", "read.delim", "read.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘GEOquery-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: getGEO > ### Title: Get a GEO object from NCBI or file > ### Aliases: getGEO > ### Keywords: IO > > ### ** Examples > > > gds <- getGEO("GDS10") > gds An object of class "GDS" channel_count [1] "1" dataset_id [1] "GDS10" "GDS10" "GDS10" "GDS10" "GDS10" "GDS10" "GDS10" "GDS10" "GDS10" [10] "GDS10" "GDS10" "GDS10" description [1] "Examination of spleen and thymus of type 1 diabetes nonobese diabetic (NOD) mouse, four NOD-derived diabetes-resistant congenic strains and two nondiabetic control strains." [2] "spleen" [3] "thymus" [4] "NOD" [5] "Idd3" [6] "Idd5" [7] "Idd3+Idd5" [8] "Idd9" [9] "B10.H2g7" [10] "B10.H2g7 Idd3" [11] "diabetic" [12] "diabetic-resistant" [13] "nondiabetic" email [1] "geo@ncbi.nlm.nih.gov" feature_count [1] "39114" institute [1] "NCBI NLM NIH" name [1] "Gene Expression Omnibus (GEO)" order [1] "none" platform [1] "GPL24" platform_organism [1] "Mus musculus" platform_technology_type [1] "in situ oligonucleotide" pubmed_id [1] "11827943" ref [1] "Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D562-6" reference_series [1] "GSE11" sample_count [1] "28" sample_id [1] "GSM582,GSM583,GSM584,GSM585,GSM586,GSM587,GSM588,GSM589,GSM590,GSM591,GSM592,GSM593,GSM594,GSM595" [2] "GSM596,GSM597,GSM598,GSM599,GSM600,GSM601,GSM602,GSM603,GSM604,GSM605,GSM606,GSM607,GSM608,GSM609" [3] "GSM582,GSM589,GSM596,GSM603" [4] "GSM583,GSM590,GSM597,GSM604" [5] "GSM584,GSM591,GSM598,GSM605" [6] "GSM585,GSM592,GSM599,GSM606" [7] "GSM586,GSM593,GSM600,GSM607" [8] "GSM587,GSM594,GSM601,GSM608" [9] "GSM588,GSM595,GSM602,GSM609" [10] "GSM582,GSM589,GSM596,GSM603" [11] "GSM583,GSM590,GSM597,GSM604,GSM584,GSM591,GSM598,GSM605,GSM585,GSM592,GSM599,GSM606,GSM586,GSM593,GSM600,GSM607" [12] "GSM587,GSM594,GSM601,GSM608,GSM588,GSM595,GSM602,GSM609" sample_organism [1] "Mus musculus" sample_type [1] "RNA" title [1] "Type 1 diabetes gene expression profiling" type [1] "Expression profiling by array" "tissue" [3] "tissue" "strain" [5] "strain" "strain" [7] "strain" "strain" [9] "strain" "strain" [11] "disease state" "disease state" [13] "disease state" update_date [1] "Jul 15 2003" value_type [1] "count" web_link [1] "http://www.ncbi.nlm.nih.gov/geo" An object of class "GEODataTable" ****** Column Descriptions ****** sample tissue strain disease.state 1 GSM582 spleen NOD diabetic 2 GSM589 spleen NOD diabetic 3 GSM583 spleen Idd3 diabetic-resistant 4 GSM590 spleen Idd3 diabetic-resistant 5 GSM584 spleen Idd5 diabetic-resistant 6 GSM591 spleen Idd5 diabetic-resistant 7 GSM585 spleen Idd3+Idd5 diabetic-resistant 8 GSM592 spleen Idd3+Idd5 diabetic-resistant 9 GSM586 spleen Idd9 diabetic-resistant 10 GSM593 spleen Idd9 diabetic-resistant 11 GSM587 spleen B10.H2g7 nondiabetic 12 GSM594 spleen B10.H2g7 nondiabetic 13 GSM588 spleen B10.H2g7 Idd3 nondiabetic 14 GSM595 spleen B10.H2g7 Idd3 nondiabetic 15 GSM596 thymus NOD diabetic 16 GSM603 thymus NOD diabetic 17 GSM597 thymus Idd3 diabetic-resistant 18 GSM604 thymus Idd3 diabetic-resistant 19 GSM598 thymus Idd5 diabetic-resistant 20 GSM605 thymus Idd5 diabetic-resistant 21 GSM599 thymus Idd3+Idd5 diabetic-resistant 22 GSM606 thymus Idd3+Idd5 diabetic-resistant 23 GSM600 thymus Idd9 diabetic-resistant 24 GSM607 thymus Idd9 diabetic-resistant 25 GSM601 thymus B10.H2g7 nondiabetic 26 GSM608 thymus B10.H2g7 nondiabetic 27 GSM602 thymus B10.H2g7 Idd3 nondiabetic 28 GSM609 thymus B10.H2g7 Idd3 nondiabetic description 1 Value for GSM582: NOD_S1; src: Spleen 2 Value for GSM589: NOD_S2; src: Spleen 3 Value for GSM583: Idd3_S1; src: Spleen 4 Value for GSM590: Idd3_S2; src: Spleen 5 Value for GSM584: Idd5_S1; src: Spleen 6 Value for GSM591: Idd5_S2; src: Spleen 7 Value for GSM585: Idd3+5_S1; src: Spleen 8 Value for GSM592: Idd3+5_S2; src: Spleen 9 Value for GSM586: Idd9_S1; src: Spleen 10 Value for GSM593: Idd9_S2; src: Spleen 11 Value for GSM587: B10.H2g7_S1; src: Spleen 12 Value for GSM594: B10.H2g7_S2; src: Spleen 13 Value for GSM588: B10.H2g7 Idd3_S1; src: Spleen 14 Value for GSM595: B10.H2g7 Idd3_S2; src: Spleen 15 Value for GSM596: NOD_T1; src: Thymus 16 Value for GSM603: NOD_T2; src: Thymus 17 Value for GSM597: Idd3_T1; src: Thymus 18 Value for GSM604: Idd3_T2; src: Thymus 19 Value for GSM598: Idd5_T1; src: Thymus 20 Value for GSM605: Idd5_T2; src: Thymus 21 Value for GSM599: Idd3+5_T1; src: Thymus 22 Value for GSM606: Idd3+5_T2; src: Thymus 23 Value for GSM600: Idd9_T1; src: Thymus 24 Value for GSM607: Idd9_T2; src: Thymus 25 Value for GSM601: B10.H2g7_T1; src: Thymus 26 Value for GSM608: B10.H2g7_T2; src: Thymus 27 Value for GSM602: B10.H2g7 Idd3_T1; src: Thymus 28 Value for GSM609: B10.H2g7 Idd3_T2; src: Thymus ****** Data Table ****** ID_REF IDENTIFIER GSM582 GSM589 GSM583 GSM590 GSM584 GSM591 GSM585 GSM592 1 1 1200011I18Rik 101 54 111 55 87 30 99 43 2 2 2 26 23 30 27 19 22 32 19 3 3 Ccdc28b NA NA NA NA NA NA NA NA 4 4 AA014405 233 162 252 178 214 144 238 147 5 5 Crebrf NA NA NA NA NA NA NA NA GSM586 GSM593 GSM587 GSM594 GSM588 GSM595 GSM596 GSM603 GSM597 GSM604 GSM598 1 105 56 43 14 112 43 97 36 117 40 125 2 24 25 14 49 32 29 31 22 26 26 35 3 NA NA NA 7 NA 4 10 22 NA 15 NA 4 250 166 86 22 236 139 216 112 241 130 270 5 NA NA NA NA NA 3 NA NA NA NA NA GSM605 GSM599 GSM606 GSM600 GSM607 GSM601 GSM608 GSM602 GSM609 1 45 99 1 109 38 87 18 72 16 2 26 18 13 25 32 28 40 14 41 3 23 NA 29 9 25 11 40 NA 22 4 144 239 148 211 139 208 16 174 15 5 NA NA NA NA NA NA NA NA NA 39109 more rows ... > > gse <- getGEO('GSE10') Found 1 file(s) GSE10_series_matrix.txt.gz Timeout was reached: [] Operation timed out after 120001 milliseconds with 1767110 bytes receivedFile stored at: /tmp/Rtmpin1uEZ/GPL4.soft.gz Error in downloadFile(myurl, destfile, mode = mode, quiet = TRUE) : Failed to download /tmp/Rtmpin1uEZ/GPL4.soft.gz! Calls: getGEO ... parseGSEMatrix -> getGEO -> getGEOfile -> downloadFile Execution halted * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 6 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/GEOquery.Rcheck/00check.log’ for details.
GEOquery.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL GEOquery ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘GEOquery’ ... ** 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 (GEOquery)
GEOquery.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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(GEOquery) Loading required package: Biobase 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, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) > > test_check("GEOquery") trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1000/suppl//GSE1000_RAW.tar?tool=geoquery' Content type 'application/x-tar' length 35307520 bytes (33.7 MB) ================================================== downloaded 33.7 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM15nnn/GSM15789/suppl//GSM15789.cel.gz?tool=geoquery' Content type 'application/x-gzip' length 3507725 bytes (3.3 MB) ================================================== downloaded 3.3 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM15nnn/GSM15789/suppl//GSM15789.cel.gz?tool=geoquery' Content type 'application/x-gzip' length 3507725 bytes (3.3 MB) ================================================== downloaded 3.3 MB [ FAIL 0 | WARN 0 | SKIP 0 | PASS 208 ] > > proc.time() user system elapsed 46.185 4.662 93.705
GEOquery.Rcheck/GEOquery-Ex.timings
name | user | system | elapsed | |
coercion | 0 | 0 | 0 | |