| Back to Build/check report for BioC 3.19 experimental data | 
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This page was generated on 2024-10-17 14:51 -0400 (Thu, 17 Oct 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" | 4763 | 
| 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 364/430 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| signatureSearchData 1.18.0  (landing page) Brendan Gongol 
 | nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | |||||||
| To the developers/maintainers of the signatureSearchData 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: signatureSearchData | 
| Version: 1.18.0 | 
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:signatureSearchData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings signatureSearchData_1.18.0.tar.gz | 
| StartedAt: 2024-10-17 12:06:09 -0400 (Thu, 17 Oct 2024) | 
| EndedAt: 2024-10-17 12:07:08 -0400 (Thu, 17 Oct 2024) | 
| EllapsedTime: 59.3 seconds | 
| RetCode: 0 | 
| Status: OK | 
| CheckDir: signatureSearchData.Rcheck | 
| Warnings: 0 | 
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:signatureSearchData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings signatureSearchData_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/signatureSearchData.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 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘signatureSearchData/DESCRIPTION’ ... OK
* this is package ‘signatureSearchData’ version ‘1.18.0’
* 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 ‘signatureSearchData’ 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 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘ExperimentHub’ ‘rhdf5’
  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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
ES_NULL 4.548  0.264   5.211
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.19-data-experiment/meat/signatureSearchData.Rcheck/00check.log’
for details.
signatureSearchData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL signatureSearchData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘signatureSearchData’ ... ** 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 (signatureSearchData)
signatureSearchData.Rcheck/signatureSearchData-Ex.timings
| name | user | system | elapsed | |
| ES_NULL | 4.548 | 0.264 | 5.211 | |
| GO_DATA | 0.693 | 0.076 | 0.949 | |
| GO_DATA_drug | 0.680 | 0.064 | 0.925 | |
| cmap | 0.037 | 0.004 | 0.041 | |
| cmap_expr | 0.036 | 0.000 | 0.036 | |
| cmap_rank | 0.036 | 0.000 | 0.036 | |
| combineNormRes | 0.001 | 0.000 | 0.001 | |
| combineResults | 0 | 0 | 0 | |
| dtlink_db_clue_sti | 0.683 | 0.076 | 0.940 | |
| getCmapCEL | 0 | 0 | 0 | |
| goAnno | 0.442 | 0.024 | 0.875 | |
| goAnno_drug | 0.392 | 0.075 | 0.646 | |
| inst_filter | 0.006 | 0.002 | 0.008 | |
| lincs | 0.036 | 0.004 | 0.039 | |
| lincs_expr | 0.043 | 0.003 | 0.047 | |
| meanExpr | 0.045 | 0.000 | 0.047 | |
| normalizeCel | 0 | 0 | 0 | |
| probe2gene | 0.000 | 0.001 | 0.001 | |
| runLimma | 1.877 | 0.113 | 1.990 | |
| sampleList | 1.466 | 0.028 | 1.494 | |
| sig_filter | 0.001 | 0.004 | 0.005 | |
| signatureSearchData | 0.688 | 0.064 | 0.934 | |
| taurefList | 0.410 | 0.038 | 1.116 | |