Levi Waldron
| Snapshot Date: 2024-12-10 07:30 -0500 (Tue, 10 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/curatedOvarianData |
| git_branch: devel |
| git_last_commit: 010dde7 |
| git_last_commit_date: 2024-10-29 09:35:36 -0500 (Tue, 29 Oct 2024) |
| Back to Build/check report for BioC 3.21 experimental data |
|
This page was generated on 2024-12-10 15:01 -0500 (Tue, 10 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4749 |
| 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 84/430 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| curatedOvarianData 1.45.0 (landing page) Levi Waldron
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | |||||||
|
To the developers/maintainers of the curatedOvarianData 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: curatedOvarianData |
| Version: 1.45.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:curatedOvarianData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings curatedOvarianData_1.45.0.tar.gz |
| StartedAt: 2024-12-10 12:05:23 -0500 (Tue, 10 Dec 2024) |
| EndedAt: 2024-12-10 12:14:14 -0500 (Tue, 10 Dec 2024) |
| EllapsedTime: 530.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: curatedOvarianData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:curatedOvarianData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings curatedOvarianData_1.45.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/curatedOvarianData.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘curatedOvarianData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘curatedOvarianData’ version ‘1.45.0’
* 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 ‘curatedOvarianData’ can be installed ... OK
* checking installed package size ... INFO
installed size is 380.8Mb
sub-directories of 1Mb or more:
data 380.4Mb
* 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 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
curatedOvarianData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL curatedOvarianData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘curatedOvarianData’ ... ** using staged installation ** data ** inst ** 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 (curatedOvarianData)
curatedOvarianData.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
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.
> require("curatedOvarianData") || stop("unable to load curatedOvarianData")
Loading required package: curatedOvarianData
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
[1] TRUE
> BiocGenerics:::testPackage("curatedOvarianData")
[1] "Checking column names in E.MTAB.386_eset"
[1] "column names OK"
[1] "Checking column names in GSE12418_eset"
[1] "column names OK"
[1] "Checking column names in GSE12470_eset"
[1] "column names OK"
[1] "Checking column names in GSE13876_eset"
[1] "column names OK"
[1] "Checking column names in GSE14764_eset"
[1] "column names OK"
[1] "Checking column names in GSE17260_eset"
[1] "column names OK"
[1] "Checking column names in GSE18520_eset"
[1] "column names OK"
[1] "Checking column names in GSE19829.GPL570_eset"
[1] "column names OK"
[1] "Checking column names in GSE19829.GPL8300_eset"
[1] "column names OK"
[1] "Checking column names in GSE20565_eset"
[1] "column names OK"
[1] "Checking column names in GSE2109_eset"
[1] "column names OK"
[1] "Checking column names in GSE26193_eset"
[1] "column names OK"
[1] "Checking column names in GSE26712_eset"
[1] "column names OK"
[1] "Checking column names in GSE30009_eset"
[1] "column names OK"
[1] "Checking column names in GSE30161_eset"
[1] "column names OK"
[1] "Checking column names in GSE32062.GPL6480_eset"
[1] "column names OK"
[1] "Checking column names in GSE32063_eset"
[1] "column names OK"
[1] "Checking column names in GSE44104_eset"
[1] "column names OK"
[1] "Checking column names in GSE49997_eset"
[1] "column names OK"
[1] "Checking column names in GSE51088_eset"
[1] "column names OK"
[1] "Checking column names in GSE6008_eset"
[1] "column names OK"
[1] "Checking column names in GSE6822_eset"
[1] "column names OK"
[1] "Checking column names in GSE8842_eset"
[1] "column names OK"
[1] "Checking column names in GSE9891_eset"
[1] "column names OK"
[1] "Checking column names in PMID15897565_eset"
[1] "column names OK"
[1] "Checking column names in PMID17290060_eset"
[1] "column names OK"
[1] "Checking column names in PMID19318476_eset"
[1] "column names OK"
[1] "Checking column names in TCGA.RNASeqV2_eset"
[1] "column names OK"
[1] "Checking column names in TCGA.mirna.8x15kv2_eset"
[1] "column names OK"
[1] "Checking column names in TCGA_eset"
[1] "column names OK"
[1] "Checking regexes in E.MTAB.386_eset"
[1] "all regex checks OK"
[1] "Checking regexes in GSE12418_eset"
[1] "all regex checks OK"
[1] "Checking regexes in GSE12470_eset"
[1] "all regex checks OK"
[1] "Checking regexes in GSE13876_eset"
[1] "all regex checks OK"
[1] "Checking regexes in GSE14764_eset"
[1] "all regex checks OK"
[1] "Checking regexes in GSE17260_eset"
[1] "all regex checks OK"
[1] "Checking regexes in GSE18520_eset"
[1] "all regex checks OK"
[1] "Checking regexes in GSE19829.GPL570_eset"
[1] "all regex checks OK"
[1] "Checking regexes in GSE19829.GPL8300_eset"
[1] "all regex checks OK"
[1] "Checking regexes in GSE20565_eset"
[1] "all regex checks OK"
[1] "Checking regexes in GSE2109_eset"
[1] "all regex checks OK"
[1] "Checking regexes in GSE26193_eset"
[1] "all regex checks OK"
[1] "Checking regexes in GSE26712_eset"
[1] "all regex checks OK"
[1] "Checking regexes in GSE30009_eset"
[1] "all regex checks OK"
[1] "Checking regexes in GSE30161_eset"
[1] "all regex checks OK"
[1] "Checking regexes in GSE32062.GPL6480_eset"
[1] "all regex checks OK"
[1] "Checking regexes in GSE32063_eset"
[1] "all regex checks OK"
[1] "Checking regexes in GSE44104_eset"
[1] "all regex checks OK"
[1] "Checking regexes in GSE49997_eset"
[1] "all regex checks OK"
[1] "Checking regexes in GSE51088_eset"
[1] "all regex checks OK"
[1] "Checking regexes in GSE6008_eset"
[1] "all regex checks OK"
[1] "Checking regexes in GSE6822_eset"
[1] "all regex checks OK"
[1] "Checking regexes in GSE8842_eset"
[1] "all regex checks OK"
[1] "Checking regexes in GSE9891_eset"
[1] "all regex checks OK"
[1] "Checking regexes in PMID15897565_eset"
[1] "all regex checks OK"
[1] "Checking regexes in PMID17290060_eset"
[1] "all regex checks OK"
[1] "Checking regexes in PMID19318476_eset"
[1] "all regex checks OK"
[1] "Checking regexes in TCGA.RNASeqV2_eset"
[1] "all regex checks OK"
[1] "Checking regexes in TCGA.mirna.8x15kv2_eset"
[1] "all regex checks OK"
[1] "Checking regexes in TCGA_eset"
[1] "all regex checks OK"
column.names variable.regex.checks
E.MTAB.386_eset TRUE TRUE
GSE12418_eset TRUE TRUE
GSE12470_eset TRUE TRUE
GSE13876_eset TRUE TRUE
GSE14764_eset TRUE TRUE
GSE17260_eset TRUE TRUE
GSE18520_eset TRUE TRUE
GSE19829.GPL570_eset TRUE TRUE
GSE19829.GPL8300_eset TRUE TRUE
GSE20565_eset TRUE TRUE
GSE2109_eset TRUE TRUE
GSE26193_eset TRUE TRUE
GSE26712_eset TRUE TRUE
GSE30009_eset TRUE TRUE
GSE30161_eset TRUE TRUE
GSE32062.GPL6480_eset TRUE TRUE
GSE32063_eset TRUE TRUE
GSE44104_eset TRUE TRUE
GSE49997_eset TRUE TRUE
GSE51088_eset TRUE TRUE
GSE6008_eset TRUE TRUE
GSE6822_eset TRUE TRUE
GSE8842_eset TRUE TRUE
GSE9891_eset TRUE TRUE
PMID15897565_eset TRUE TRUE
PMID17290060_eset TRUE TRUE
PMID19318476_eset TRUE TRUE
TCGA.RNASeqV2_eset TRUE TRUE
TCGA.mirna.8x15kv2_eset TRUE TRUE
TCGA_eset TRUE TRUE
i df...i. dfref...i.
1 1 15897565 15897565
2 1 16996261 16996261
3 1 17290060 17290060
4 1 18593951 18593951
5 1 18698038 18698038
6 1 19047114 19047114
7 1 19192944 19192944
8 1 19294737 19294737
9 1 19318476 19318476
10 1 19440550 19440550
11 1 19486012 19486012
12 1 19962670 19962670
13 1 20300634 20300634
14 1 20492709 20492709
15 1 20547991 20547991
16 1 20547991 20547991
17 1 21720365 21720365
18 1 21720365 21720365
19 1 21720365 21720365
20 1 22101765 22101765
21 1 22241791 22241791
22 1 22241791 22241791
23 1 22348002 22348002
24 1 22348014 22348014
25 1 22492981 22492981
26 1 22497737 22497737
27 1 23934190 23934190
28 1 24368280 24368280
29 1 PMID unknown PMID unknown
30 1 PMID unknown PMID unknown
i df...i. dfref...i.
1 2 63 63
2 2 54 54
3 2 117 117
4 2 195 195
5 2 285 285
6 2 83 83
7 2 157 157
8 2 80 80
9 2 42 42
10 2 103 103
11 2 53 53
12 2 63 63
13 2 110 110
14 2 140 140
15 2 28 28
16 2 42 42
17 2 261 261
18 2 554 554
19 2 578 578
20 2 107 107
21 2 40 40
22 2 260 260
23 2 129 129
24 2 58 58
25 2 103 103
26 2 204 204
27 2 60 60
28 2 172 172
29 2 66 66
30 2 204 204
i df...i. dfref...i.
1 3 13104 13104
2 3 12681 12681
3 3 13104 13104
4 3 13104 13104
5 3 19816 19816
6 3 6536 6536
7 3 20577 20577
8 3 13104 13104
9 3 13104 13104
10 3 13104 13104
11 3 16889 16889
12 3 19816 19816
13 3 20106 20106
14 3 19816 19816
15 3 19816 19816
16 3 8995 8995
17 3 20502 20502
18 3 799 799
19 3 13104 13104
20 3 19816 19816
21 3 20106 20106
22 3 20106 20106
23 3 10357 10357
24 3 19816 19816
25 3 359 359
26 3 16048 16048
27 3 19816 19816
28 3 8211 8211
29 3 5251 5251
30 3 19816 19816
i df...i. dfref...i.
1 4 63 63
2 4 0 0
3 4 117 117
4 4 195 195
5 4 285 285
6 4 0 0
7 4 0 0
8 4 80 80
9 4 42 42
10 4 103 103
11 4 0 0
12 4 63 63
13 4 0 0
14 4 140 140
15 4 28 28
16 4 42 42
17 4 0 0
18 4 0 0
19 4 577 577
20 4 107 107
21 4 0 0
22 4 0 0
23 4 0 0
24 4 58 58
25 4 0 0
26 4 0 0
27 4 60 60
28 4 0 0
29 4 66 66
30 4 204 204
i df...i. dfref...i.
1 5 0 0
2 5 0 0
3 5 67 67
4 5 129 129
5 5 113 113
6 5 15 15
7 5 113 113
8 5 21 21
9 5 22 22
10 5 0 0
11 5 0 0
12 5 41 41
13 5 46 46
14 5 0 0
15 5 17 17
16 5 23 23
17 5 143 143
18 5 286 286
19 5 290 290
20 5 76 76
21 5 22 22
22 5 121 121
23 5 73 73
24 5 36 36
25 5 57 57
26 5 57 57
27 5 0 0
28 5 112 112
29 5 0 0
30 5 0 0
RUNIT TEST PROTOCOL -- Tue Dec 10 12:12:13 2024
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
curatedOvarianData RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
77.476 1.060 78.528
curatedOvarianData.Rcheck/curatedOvarianData-Ex.timings
| name | user | system | elapsed | |
| curatedOvarianData-package | 0.022 | 0.004 | 0.027 | |