Build/check report for BioC 3.19 experimental data - CHECK results for healthyControlsPresenceChecker on nebbiolo1

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*

CHECK results for healthyControlsPresenceChecker on nebbiolo1

To the developers/maintainers of the healthyControlsPresenceChecker 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.

raw results

Summary

Package: healthyControlsPresenceChecker

Version: 1.8.0

Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:healthyControlsPresenceChecker.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings healthyControlsPresenceChecker_1.8.0.tar.gz

StartedAt: 2024-10-17 11:30:44 -0400 (Thu, 17 Oct 2024)

EndedAt: 2024-10-17 11:32:33 -0400 (Thu, 17 Oct 2024)

EllapsedTime: 109.7 seconds

RetCode: 0

Status: OK

CheckDir: healthyControlsPresenceChecker.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:healthyControlsPresenceChecker.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings healthyControlsPresenceChecker_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/healthyControlsPresenceChecker.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 ‘healthyControlsPresenceChecker/DESCRIPTION’ ... OK
* this is package ‘healthyControlsPresenceChecker’ version ‘1.8.0’
* 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 ‘healthyControlsPresenceChecker’ 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 ... 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 ... 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: OK

Installation output

healthyControlsPresenceChecker.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL healthyControlsPresenceChecker
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘healthyControlsPresenceChecker’ ...
** 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 (healthyControlsPresenceChecker)

Tests output

healthyControlsPresenceChecker.Rcheck/tests/runTests.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.

> BiocGenerics:::testPackage("healthyControlsPresenceChecker")
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Processed URL: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE19nnn/GSE19429
Found 1 file(s)
GSE19429_series_matrix.txt.gz
Healthy control 1: 
Healthy control 10: 
Healthy control 11: 
Healthy control 12: 
Healthy control 13: 
Healthy control 14: 
Healthy control 15: 
Healthy control 16: 
Healthy control 17: 
Healthy control 2: 
Healthy control 3: 
Healthy control 4: 
Healthy control 5: 
Healthy control 6: 
Healthy control 7: 
Healthy control 8: 
Healthy control 9: 
MDS patient 1: 
MDS patient 10: 
MDS patient 100: 
MDS patient 101: 
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MDS patient 99: 
disease status: healthy control: 
disease status: myelodysplastic syndromes (MDS): 
50 ng of total RNA were amplified and biotin-labelled with the Two-Cycle cDNA Synthesis and the Two-Cycle Target Labelling and Control Reagent packages according to the standard Affymetrix protocol.: 
healthy control: 
myelodysplastic syndromes (MDS): 
Processed URL: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58831
Found 1 file(s)
GSE58831_series_matrix.txt.gz
disease status: Healthy control: 
disease status: MDS: 
50 ng of total RNA were amplified and biotin-labelled with the Two-Cycle cDNA Synthesis and the Two-Cycle Target Labelling and Control Reagent packages according to the standard Affymetrix protocol: 
Healthy control 1: 
Healthy control 10: 
Healthy control 11: 
Healthy control 12: 
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Healthy control 2: 
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MDS patient 101: 
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Healthy control: 
MDS: 
Processed URL: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE19nnn/GSE19429
Found 1 file(s)
GSE19429_series_matrix.txt.gz
Using locally cached version: /tmp/Rtmp8zRJIn/GSE19429_series_matrix.txt.gz
Healthy control 1: 
Healthy control 10: 
Healthy control 11: 
Healthy control 12: 
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Healthy control 2: 
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MDS patient 1: 
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MDS patient 95: 
MDS patient 96: 
MDS patient 97: 
MDS patient 98: 
MDS patient 99: 
disease status: healthy control: 
disease status: myelodysplastic syndromes (MDS): 
50 ng of total RNA were amplified and biotin-labelled with the Two-Cycle cDNA Synthesis and the Two-Cycle Target Labelling and Control Reagent packages according to the standard Affymetrix protocol.: 
healthy control: 
myelodysplastic syndromes (MDS): 
Processed URL: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34111
Found 1 file(s)
GSE34111_series_matrix.txt.gz
Control quadriceps muscle sample Sample100: 
Control quadriceps muscle sample Sample73: 
Control quadriceps muscle sample Sample75: 
Control quadriceps muscle sample Sample79: 
Control quadriceps muscle sample Sample94: 
Control quadriceps muscle sample Sample99: 
Post-op quadriceps muscle sample Sample61: 
Post-op quadriceps muscle sample Sample62: 
Post-op quadriceps muscle sample Sample63: 
Post-op quadriceps muscle sample Sample64: 
Post-op quadriceps muscle sample Sample65: 
Post-op quadriceps muscle sample Sample68: 
Post-op quadriceps muscle sample Sample70: 
Post-op quadriceps muscle sample Sample82: 
Post-op quadriceps muscle sample Sample84: 
Post-op quadriceps muscle sample Sample88: 
Post-op quadriceps muscle sample Sample92: 
Post-op quadriceps muscle sample Sample97: 
Pre-op quadriceps muscle sample Sample12: 
Pre-op quadriceps muscle sample Sample13: 
Pre-op quadriceps muscle sample Sample20: 
Pre-op quadriceps muscle sample Sample24: 
Pre-op quadriceps muscle sample Sample34: 
Pre-op quadriceps muscle sample Sample4: 
Pre-op quadriceps muscle sample Sample47: 
Pre-op quadriceps muscle sample Sample78: 
Pre-op quadriceps muscle sample Sample80: 
Pre-op quadriceps muscle sample Sample87: 
Pre-op quadriceps muscle sample Sample91: 
Pre-op quadriceps muscle sample Sample95: 
quadriceps muscle biopsy healthy control: 
quadriceps muscle biopsy post operative: 
quadriceps muscle biopsy pre operative: 
condition: cancer: 
condition: cancer-free: 
condition: healthy control: 
Control quadriceps muscle sample: 
Post-op quadriceps muscle sample: 
Pre-op quadriceps muscle sample: 
cancer: 
cancer-free: 
healthy control: 
Processed URL: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE47nnn/GSE47407
Found 1 file(s)
GSE47407_series_matrix.txt.gz
URL caused a warning: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE32123131nnn/GSE32123131231
cannot open URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE32123131nnn/GSE32123131231': HTTP status was '404 Not Found'Processed URL: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE32123131nnn/GSE32123131231
The web url https://ftp.ncbi.nlm.nih.gov/geo/series/GSE32123131nnn/GSE32123131231 is unavailable right now (Error 404 webpage not found). The GEO code might be wrong. The function will stop here



RUNIT TEST PROTOCOL -- Thu Oct 17 11:32:24 2024 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
healthyControlsPresenceChecker RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 34.970   4.349  67.469

Example timings

healthyControlsPresenceChecker.Rcheck/healthyControlsPresenceChecker-Ex.timings

name	user	system	elapsed
healthyControlsCheck	0.746	0.043	2.346