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

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.

raw results

Summary

Package: curatedOvarianData

Version: 1.42.0

Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:curatedOvarianData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings curatedOvarianData_1.42.0.tar.gz

StartedAt: 2024-10-17 11:12:25 -0400 (Thu, 17 Oct 2024)

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

EllapsedTime: 304.8 seconds

RetCode: 0

Status: OK

CheckDir: curatedOvarianData.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:curatedOvarianData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings curatedOvarianData_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/curatedOvarianData.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 ‘curatedOvarianData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘curatedOvarianData’ version ‘1.42.0’
* 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 ‘curatedOvarianData’ can be installed ... OK
* checking installed package size ... NOTE
  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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-data-experiment/meat/curatedOvarianData.Rcheck/00check.log’
for details.

Installation output

curatedOvarianData.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.19-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)

Tests output

curatedOvarianData.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.

> require("curatedOvarianData") || stop("unable to load curatedOvarianData")
Loading required package: curatedOvarianData
Loading required package: Biobase
Loading required package: BiocGenerics

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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 -- Thu Oct 17 11:15:31 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 
 76.092   1.265  77.364

Example timings

curatedOvarianData.Rcheck/curatedOvarianData-Ex.timings

name	user	system	elapsed
curatedOvarianData-package	0.019	0.007	0.026