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This page was generated on 2023-10-20 09:38:13 -0400 (Fri, 20 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
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 1988/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SpidermiR 1.30.0 (landing page) Claudia Cava
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | ERROR | OK | ||||||||
To the developers/maintainers of the SpidermiR package: - 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: SpidermiR |
Version: 1.30.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpidermiR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpidermiR_1.30.0.tar.gz |
StartedAt: 2023-10-19 03:50:15 -0400 (Thu, 19 Oct 2023) |
EndedAt: 2023-10-19 03:56:20 -0400 (Thu, 19 Oct 2023) |
EllapsedTime: 364.1 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: SpidermiR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpidermiR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpidermiR_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SpidermiR.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SpidermiR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SpidermiR’ version ‘1.30.0’ * 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 ‘SpidermiR’ can be installed ... OK * checking installed package size ... OK * checking package 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 Namespace in Imports field not imported from: ‘gdata’ All declared Imports should be used. * 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 examples ... ERROR Running examples in ‘SpidermiR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: SpidermiRquery_disease > ### Title: Visualize disease categories > ### Aliases: SpidermiRquery_disease > > ### ** Examples > > disease<-SpidermiRquery_disease(diseaseID) Warning in file(file, "rt") : URL 'http://www.cuilab.cn/static/hmdd3/data/alldata.txt': status was 'Failure when receiving data from the peer' Error in file(file, "rt") : cannot open the connection to 'http://www.cuilab.cn/static/hmdd3/data/alldata.txt' Calls: SpidermiRquery_disease -> read.delim -> read.table -> file Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SpidermiR.Rcheck/00check.log’ for details.
SpidermiR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpidermiR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘SpidermiR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (SpidermiR)
SpidermiR.Rcheck/SpidermiR-Ex.timings
name | user | system | elapsed | |
SpidermiRanalyze_degree_centrality | 0.003 | 0.000 | 0.008 | |
SpidermiRanalyze_direct_net | 0.004 | 0.001 | 0.008 | |
SpidermiRanalyze_direct_subnetwork | 0.006 | 0.002 | 0.030 | |
SpidermiRanalyze_subnetwork_neigh | 0.004 | 0.002 | 0.005 | |
SpidermiRdownload_drug_gene | 1.392 | 0.064 | 9.556 | |
SpidermiRdownload_miRNAprediction | 7.407 | 0.759 | 15.426 | |
SpidermiRdownload_net | 0.187 | 0.015 | 8.916 | |
SpidermiRprepare_NET | 0.727 | 0.021 | 2.923 | |