##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:healthyControlsPresenceChecker.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings healthyControlsPresenceChecker_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-data-experiment/meat/healthyControlsPresenceChecker.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘healthyControlsPresenceChecker/DESCRIPTION’ ... OK
* this is package ‘healthyControlsPresenceChecker’ version ‘1.0.0’
* 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 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 ... 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 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: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL healthyControlsPresenceChecker
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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)

R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

> 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: 
MDS patient 102: 
MDS patient 103: 
MDS patient 104: 
MDS patient 105: 
MDS patient 106: 
MDS patient 107: 
MDS patient 108: 
MDS patient 109: 
MDS patient 11: 
MDS patient 110: 
MDS patient 111: 
MDS patient 112: 
MDS patient 113: 
MDS patient 114: 
MDS patient 115: 
MDS patient 116: 
MDS patient 117: 
MDS patient 118: 
MDS patient 119: 
MDS patient 12: 
MDS patient 120: 
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MDS patient 123: 
MDS patient 124: 
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MDS patient 130: 
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MDS patient 177: 
MDS patient 178: 
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MDS patient 183: 
MDS patient 19: 
MDS patient 2: 
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MDS patient 88: 
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MDS patient 9: 
MDS patient 90: 
MDS patient 91: 
MDS patient 92: 
MDS patient 93: 
MDS patient 94: 
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/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: 
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 101: 
MDS patient 102: 
MDS patient 103: 
MDS patient 104: 
MDS patient 106: 
MDS patient 107: 
MDS patient 108: 
MDS patient 11: 
MDS patient 113: 
MDS patient 114: 
MDS patient 115: 
MDS patient 116: 
MDS patient 117: 
MDS patient 118: 
MDS patient 12: 
MDS patient 120: 
MDS patient 121: 
MDS patient 123: 
MDS patient 124: 
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MDS patient 127: 
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MDS patient 150: 
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MDS patient 90: 
MDS patient 91: 
MDS patient 92: 
MDS patient 94: 
MDS patient 96: 
MDS patient 97: 
MDS patient 98: 
MDS patient 99: 
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/Rtmp5GCGzr/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: 
MDS patient 102: 
MDS patient 103: 
MDS patient 104: 
MDS patient 105: 
MDS patient 106: 
MDS patient 107: 
MDS patient 108: 
MDS patient 109: 
MDS patient 11: 
MDS patient 110: 
MDS patient 111: 
MDS patient 112: 
MDS patient 113: 
MDS patient 114: 
MDS patient 115: 
MDS patient 116: 
MDS patient 117: 
MDS patient 118: 
MDS patient 119: 
MDS patient 12: 
MDS patient 120: 
MDS patient 121: 
MDS patient 122: 
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MDS patient 126: 
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MDS patient 141: 
MDS patient 142: 
MDS patient 143: 
MDS patient 144: 
MDS patient 145: 
MDS patient 146: 
MDS patient 147: 
MDS patient 148: 
MDS patient 149: 
MDS patient 15: 
MDS patient 150: 
MDS patient 151: 
MDS patient 152: 
MDS patient 153: 
MDS patient 154: 
MDS patient 155: 
MDS patient 156: 
MDS patient 157: 
MDS patient 158: 
MDS patient 159: 
MDS patient 16: 
MDS patient 160: 
MDS patient 161: 
MDS patient 162: 
MDS patient 163: 
MDS patient 164: 
MDS patient 165: 
MDS patient 166: 
MDS patient 167: 
MDS patient 168: 
MDS patient 169: 
MDS patient 17: 
MDS patient 170: 
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MDS patient 177: 
MDS patient 178: 
MDS patient 179: 
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MDS patient 180: 
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MDS patient 183: 
MDS patient 19: 
MDS patient 2: 
MDS patient 20: 
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MDS patient 24: 
MDS patient 25: 
MDS patient 26: 
MDS patient 27: 
MDS patient 28: 
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MDS patient 3: 
MDS patient 30: 
MDS patient 31: 
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MDS patient 34: 
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MDS patient 4: 
MDS patient 40: 
MDS patient 41: 
MDS patient 42: 
MDS patient 43: 
MDS patient 44: 
MDS patient 45: 
MDS patient 46: 
MDS patient 47: 
MDS patient 48: 
MDS patient 49: 
MDS patient 5: 
MDS patient 50: 
MDS patient 51: 
MDS patient 52: 
MDS patient 53: 
MDS patient 54: 
MDS patient 55: 
MDS patient 56: 
MDS patient 57: 
MDS patient 58: 
MDS patient 59: 
MDS patient 6: 
MDS patient 60: 
MDS patient 61: 
MDS patient 62: 
MDS patient 63: 
MDS patient 64: 
MDS patient 65: 
MDS patient 66: 
MDS patient 67: 
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MDS patient 7: 
MDS patient 70: 
MDS patient 71: 
MDS patient 72: 
MDS patient 73: 
MDS patient 74: 
MDS patient 75: 
MDS patient 76: 
MDS patient 77: 
MDS patient 78: 
MDS patient 79: 
MDS patient 8: 
MDS patient 80: 
MDS patient 81: 
MDS patient 82: 
MDS patient 83: 
MDS patient 84: 
MDS patient 85: 
MDS patient 86: 
MDS patient 87: 
MDS patient 88: 
MDS patient 89: 
MDS patient 9: 
MDS patient 90: 
MDS patient 91: 
MDS patient 92: 
MDS patient 93: 
MDS patient 94: 
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 -- Tue Oct 18 11:26:38 2022 
*********************************************** 
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 
 33.917   3.985  65.296