| Back to Build/check report for BioC 3.20 experimental data |
|
This page was generated on 2024-12-10 15:42 -0500 (Tue, 10 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4739 |
| 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 177/431 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| healthyControlsPresenceChecker 1.10.0 (landing page) Davide Chicco
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | |||||||
|
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. |
| Package: healthyControlsPresenceChecker |
| Version: 1.10.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:healthyControlsPresenceChecker.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings healthyControlsPresenceChecker_1.10.0.tar.gz |
| StartedAt: 2024-12-10 12:36:34 -0500 (Tue, 10 Dec 2024) |
| EndedAt: 2024-12-10 12:42:37 -0500 (Tue, 10 Dec 2024) |
| EllapsedTime: 362.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: healthyControlsPresenceChecker.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:healthyControlsPresenceChecker.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings healthyControlsPresenceChecker_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/healthyControlsPresenceChecker.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘healthyControlsPresenceChecker/DESCRIPTION’ ... OK
* this is package ‘healthyControlsPresenceChecker’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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
healthyControlsPresenceChecker.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL healthyControlsPresenceChecker ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-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)
healthyControlsPresenceChecker.Rcheck/tests/runTests.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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:
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:
MDS patient 123:
MDS patient 124:
MDS patient 125:
MDS patient 126:
MDS patient 127:
MDS patient 128:
MDS patient 129:
MDS patient 13:
MDS patient 130:
MDS patient 131:
MDS patient 132:
MDS patient 133:
MDS patient 134:
MDS patient 135:
MDS patient 136:
MDS patient 137:
MDS patient 138:
MDS patient 139:
MDS patient 14:
MDS patient 140:
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:
MDS patient 171:
MDS patient 172:
MDS patient 173:
MDS patient 174:
MDS patient 175:
MDS patient 176:
MDS patient 177:
MDS patient 178:
MDS patient 179:
MDS patient 18:
MDS patient 180:
MDS patient 181:
MDS patient 182:
MDS patient 183:
MDS patient 19:
MDS patient 2:
MDS patient 20:
MDS patient 21:
MDS patient 22:
MDS patient 23:
MDS patient 24:
MDS patient 25:
MDS patient 26:
MDS patient 27:
MDS patient 28:
MDS patient 29:
MDS patient 3:
MDS patient 30:
MDS patient 31:
MDS patient 32:
MDS patient 33:
MDS patient 34:
MDS patient 35:
MDS patient 36:
MDS patient 37:
MDS patient 38:
MDS patient 39:
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:
MDS patient 68:
MDS patient 69:
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/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:
MDS patient 125:
MDS patient 127:
MDS patient 128:
MDS patient 129:
MDS patient 130:
MDS patient 131:
MDS patient 132:
MDS patient 133:
MDS patient 134:
MDS patient 135:
MDS patient 136:
MDS patient 138:
MDS patient 139:
MDS patient 14:
MDS patient 140:
MDS patient 141:
MDS patient 142:
MDS patient 143:
MDS patient 144:
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 155:
MDS patient 156:
MDS patient 157:
MDS patient 158:
MDS patient 159:
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 170:
MDS patient 171:
MDS patient 172:
MDS patient 173:
MDS patient 174:
MDS patient 176:
MDS patient 178:
MDS patient 179:
MDS patient 180:
MDS patient 181:
MDS patient 183:
MDS patient 184:
MDS patient 185:
MDS patient 186:
MDS patient 187:
MDS patient 188:
MDS patient 189:
MDS patient 190:
MDS patient 191:
MDS patient 192:
MDS patient 193:
MDS patient 194:
MDS patient 195:
MDS patient 196:
MDS patient 197:
MDS patient 198:
MDS patient 199:
MDS patient 200:
MDS patient 201:
MDS patient 202:
MDS patient 203:
MDS patient 204:
MDS patient 205:
MDS patient 206:
MDS patient 207:
MDS patient 208:
MDS patient 209:
MDS patient 210:
MDS patient 211:
MDS patient 212:
MDS patient 213:
MDS patient 214:
MDS patient 215:
MDS patient 216:
MDS patient 217:
MDS patient 218:
MDS patient 219:
MDS patient 220:
MDS patient 221:
MDS patient 222:
MDS patient 223:
MDS patient 224:
MDS patient 225:
MDS patient 226:
MDS patient 25:
MDS patient 27:
MDS patient 29:
MDS patient 33:
MDS patient 43:
MDS patient 50:
MDS patient 52:
MDS patient 53:
MDS patient 54:
MDS patient 55:
MDS patient 57:
MDS patient 58:
MDS patient 59:
MDS patient 61:
MDS patient 62:
MDS patient 63:
MDS patient 66:
MDS patient 67:
MDS patient 68:
MDS patient 69:
MDS patient 71:
MDS patient 72:
MDS patient 74:
MDS patient 75:
MDS patient 76:
MDS patient 79:
MDS patient 80:
MDS patient 81:
MDS patient 82:
MDS patient 84:
MDS patient 85:
MDS patient 87:
MDS patient 88:
MDS patient 89:
MDS patient 9:
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: /home/biocbuild/bbs-3.20-data-experiment/tmpdir/RtmpwHHav7/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:
MDS patient 123:
MDS patient 124:
MDS patient 125:
MDS patient 126:
MDS patient 127:
MDS patient 128:
MDS patient 129:
MDS patient 13:
MDS patient 130:
MDS patient 131:
MDS patient 132:
MDS patient 133:
MDS patient 134:
MDS patient 135:
MDS patient 136:
MDS patient 137:
MDS patient 138:
MDS patient 139:
MDS patient 14:
MDS patient 140:
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:
MDS patient 171:
MDS patient 172:
MDS patient 173:
MDS patient 174:
MDS patient 175:
MDS patient 176:
MDS patient 177:
MDS patient 178:
MDS patient 179:
MDS patient 18:
MDS patient 180:
MDS patient 181:
MDS patient 182:
MDS patient 183:
MDS patient 19:
MDS patient 2:
MDS patient 20:
MDS patient 21:
MDS patient 22:
MDS patient 23:
MDS patient 24:
MDS patient 25:
MDS patient 26:
MDS patient 27:
MDS patient 28:
MDS patient 29:
MDS patient 3:
MDS patient 30:
MDS patient 31:
MDS patient 32:
MDS patient 33:
MDS patient 34:
MDS patient 35:
MDS patient 36:
MDS patient 37:
MDS patient 38:
MDS patient 39:
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:
MDS patient 68:
MDS patient 69:
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 Dec 10 12:42:21 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
43.238 4.622 70.262
healthyControlsPresenceChecker.Rcheck/healthyControlsPresenceChecker-Ex.timings
| name | user | system | elapsed | |
| healthyControlsCheck | 1.299 | 0.032 | 2.589 | |