Panagiotis Moulos
| Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/sitadela |
| git_branch: devel |
| git_last_commit: 407ddcf |
| git_last_commit_date: 2024-04-30 11:32:08 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-16 11:41 -0400 (Tue, 16 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
| 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 1945/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sitadela 1.13.0 (landing page) Panagiotis Moulos
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
|
To the developers/maintainers of the sitadela package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sitadela.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: sitadela |
| Version: 1.13.0 |
| Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sitadela.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings sitadela_1.13.0.tar.gz |
| StartedAt: 2024-07-16 04:23:12 -0400 (Tue, 16 Jul 2024) |
| EndedAt: 2024-07-16 04:32:09 -0400 (Tue, 16 Jul 2024) |
| EllapsedTime: 537.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sitadela.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sitadela.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings sitadela_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/sitadela.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'sitadela/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sitadela' version '1.13.0'
* 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 whether package 'sitadela' 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 whether startup messages can be suppressed ... NOTE
sitadela database found at C:/Users/biocbuild/AppData/Roaming/R/data/R/sitadela directory
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
testFuns 5.22 0.3 5.97
getAnnotation 3.78 0.3 9.38
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.20-bioc/meat/sitadela.Rcheck/00check.log'
for details.
sitadela.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL sitadela ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'sitadela' ... ** 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 sitadela database found at C:/Users/biocbuild/AppData/Roaming/R/data/R/sitadela directory ** testing if installed package can be loaded from final location sitadela database found at C:/Users/biocbuild/AppData/Roaming/R/data/R/sitadela directory ** testing if installed package keeps a record of temporary installation path * DONE (sitadela)
sitadela.Rcheck/tests/runTests.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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("sitadela")
sitadela database found at C:/Users/biocbuild/AppData/Roaming/R/data/R/sitadela directory
Scheduling 1 tests
==================================================
Running test 1 of 1 scheduled
Testing level gene from mm10 from latest version
Using Ensembl host https://jan2024.archive.ensembl.org
Test 1 successful!
Created 57089 features
Sample data:
chromosome start end gene_id gc_content
ENSMUSG00000102693 chr1 3143476 3144545 ENSMUSG00000102693 34.21
ENSMUSG00000064842 chr1 3172239 3172348 ENSMUSG00000064842 36.36
ENSMUSG00000051951 chr1 3276124 3741721 ENSMUSG00000051951 38.51
ENSMUSG00000102851 chr1 3322980 3323459 ENSMUSG00000102851 39.79
ENSMUSG00000103377 chr1 3435954 3438772 ENSMUSG00000103377 40.79
ENSMUSG00000104017 chr1 3445779 3448011 ENSMUSG00000104017 36.99
strand gene_name biotype
ENSMUSG00000102693 + 4933401J01Rik TEC
ENSMUSG00000064842 + Gm26206 snRNA
ENSMUSG00000051951 - Xkr4 protein_coding
ENSMUSG00000102851 + Gm18956 processed_pseudogene
ENSMUSG00000103377 - Gm37180 TEC
ENSMUSG00000104017 - Gm37363 TEC
Testing finished!
Summary
==================================================
Succesful tests: 1 out of 1
Failed tests : 0 out of 1
Scheduling 1 tests
==================================================
Running test 1 of 1 scheduled
Testing level transcript from mm10 from latest version
Using Ensembl host https://jan2024.archive.ensembl.org
Test 1 successful!
Created 149039 features
Sample data:
chromosome start end transcript_id
ENSMUST00000193812 chr1 3143476 3144545 ENSMUST00000193812
ENSMUST00000082908 chr1 3172239 3172348 ENSMUST00000082908
ENSMUST00000162897 chr1 3276124 3286567 ENSMUST00000162897
ENSMUST00000159265 chr1 3276746 3285855 ENSMUST00000159265
ENSMUST00000070533 chr1 3284705 3741721 ENSMUST00000070533
ENSMUST00000192857 chr1 3322980 3323459 ENSMUST00000192857
gene_id strand gene_name biotype
ENSMUST00000193812 ENSMUSG00000102693 + 4933401J01Rik TEC
ENSMUST00000082908 ENSMUSG00000064842 + Gm26206 snRNA
ENSMUST00000162897 ENSMUSG00000051951 - Xkr4 protein_coding
ENSMUST00000159265 ENSMUSG00000051951 - Xkr4 protein_coding
ENSMUST00000070533 ENSMUSG00000051951 - Xkr4 protein_coding
ENSMUST00000192857 ENSMUSG00000102851 + Gm18956 processed_pseudogene
Testing finished!
Summary
==================================================
Succesful tests: 1 out of 1
Failed tests : 0 out of 1
Scheduling 1 tests
==================================================
Running test 1 of 1 scheduled
Testing level gene from danrer11 from latest version
Using Ensembl host https://jan2024.archive.ensembl.org
Test 1 successful!
Created 32020 features
Sample data:
chromosome start end gene_id gc_content strand
ENSDARG00000099104 chr1 6408 12027 ENSDARG00000099104 43.42 -
ENSDARG00000102407 chr1 11822 16373 ENSDARG00000102407 54.39 +
ENSDARG00000102097 chr1 18716 23389 ENSDARG00000102097 52.70 +
ENSDARG00000099319 chr1 25585 27255 ENSDARG00000099319 37.64 +
ENSDARG00000099640 chr1 27690 34330 ENSDARG00000099640 53.02 +
ENSDARG00000104071 chr1 36552 39191 ENSDARG00000104071 50.64 +
gene_name biotype
ENSDARG00000099104 rpl24 protein_coding
ENSDARG00000102407 cep97 protein_coding
ENSDARG00000102097 nfkbiz protein_coding
ENSDARG00000099319 CU651657.1 protein_coding
ENSDARG00000099640 eed protein_coding
ENSDARG00000104071 hikeshi protein_coding
Testing finished!
Summary
==================================================
Succesful tests: 1 out of 1
Failed tests : 0 out of 1
Scheduling 1 tests
==================================================
Running test 1 of 1 scheduled
Testing level transcript from danrer11 from latest version
Using Ensembl host https://jan2024.archive.ensembl.org
Test 1 successful!
Created 59253 features
Sample data:
chromosome start end transcript_id gene_id
ENSDART00000164359 chr1 6408 12027 ENSDART00000164359 ENSDARG00000099104
ENSDART00000157701 chr1 6642 9919 ENSDART00000157701 ENSDARG00000099104
ENSDART00000158290 chr1 6642 7335 ENSDART00000158290 ENSDARG00000099104
ENSDART00000167898 chr1 6644 11725 ENSDART00000167898 ENSDARG00000099104
ENSDART00000166393 chr1 11822 16373 ENSDART00000166393 ENSDARG00000102407
ENSDART00000161842 chr1 11992 14058 ENSDART00000161842 ENSDARG00000102407
strand gene_name biotype
ENSDART00000164359 - rpl24 protein_coding
ENSDART00000157701 - rpl24 protein_coding
ENSDART00000158290 - rpl24 protein_coding
ENSDART00000167898 - rpl24 protein_coding
ENSDART00000166393 + cep97 protein_coding
ENSDART00000161842 + cep97 protein_coding
Testing finished!
Summary
==================================================
Succesful tests: 1 out of 1
Failed tests : 0 out of 1
Scheduling 2 tests
==================================================
Running test 1 of 2 scheduled
Opening sitadela SQLite database C:\Users\biocbuild\bbs-3.20-bioc\tmpdir\RtmpWyYp6k\file358301d096e44
Importing GTF C:/Users/biocbuild/bbs-3.20-bioc/R/library/sitadela/dummy.gtf.gz as GTF to make id map
Making id map
Importing GTF C:/Users/biocbuild/bbs-3.20-bioc/R/library/sitadela/dummy.gtf.gz as TxDb
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Retrieving gene annotation for dummy from dummy_db version 1 from C:/Users/biocbuild/bbs-3.20-bioc/R/library/sitadela/dummy.gtf.gz
Retrieving transcript annotation for dummy from dummy_db version 1
Retrieving summarized transcript annotation for dummy from dummy_db version 1
Retrieving 3' UTR annotation for dummy from dummy_db version 1
Retrieving summarized 3' UTR annotation per gene for dummy from dummy_db version 1
Retrieving summarized 3' UTR annotation per transcript for dummy from dummy_db version 1
Retrieving exon annotation for dummy from dummy_db version 1
Retrieving summarized exon annotation for dummy from dummy_db version 1
Retrieving extended exon annotation for dummy from dummy_db version 1
Retrieving summarized transcript exon annotation for dummy from dummy_db version 1
Test 1 successful!
Running test 2 of 2 scheduled
Test 2 successful!
Deleting temporary database C:\Users\biocbuild\bbs-3.20-bioc\tmpdir\RtmpWyYp6k\file358301d096e44
Scheduling 2 tests
==================================================
Running test 1 of 2 scheduled
********************************************************
This is sitadela 1.13.0 genomic region annotation builder
********************************************************
sitadela database found at C:/Users/biocbuild/bbs-3.20-bioc/tmpdir/RtmpWyYp6k directory
========================================================
2024-07-16 04:30:59 - Try 1
========================================================
Opening sitadela SQLite database C:\Users\biocbuild\bbs-3.20-bioc\tmpdir\RtmpWyYp6k\file3583039f1496
Retrieving genome information for dm6 from ensembl
Retrieving gene annotation for dm6 from ensembl version 102
Using Ensembl host https://nov2020.archive.ensembl.org
Retrieving transcript annotation for dm6 from ensembl version 102
Using Ensembl host https://nov2020.archive.ensembl.org
Merging transcripts for dm6 from ensembl version 102
Retrieving 3' UTR annotation for dm6 from ensembl version 102
Using Ensembl host https://nov2020.archive.ensembl.org
Merging gene 3' UTRs for dm6 from ensembl version 102
Merging transcript 3' UTRs for dm6 from ensembl version 102
Retrieving exon annotation for dm6 from ensembl version 102
Using Ensembl host https://nov2020.archive.ensembl.org
Retrieving extended exon annotation for dm6 from ensembl version 102
Using Ensembl host https://nov2020.archive.ensembl.org
Merging exons for dm6 from ensembl version 102
Merging exons for dm6 from ensembl version 102
-------------------------------------------------------
Building process complete!
-------------------------------------------------------
Test 1 successful!
Running test 2 of 2 scheduled
Test 2 successful!
Deleting temporary database C:\Users\biocbuild\bbs-3.20-bioc\tmpdir\RtmpWyYp6k\file3583039f1496
Loading required package: RMySQL
Loading required package: DBI
Cannot run 3' UTR tests from UCSC on non Unix/Linux machines!
Cannot run 3' UTR tests from UCSC on non Unix/Linux machines!
Cannot run 3' UTR tests from UCSC on non Unix/Linux machines!
Cannot run 3' UTR tests from UCSC on non Unix/Linux machines!
Cannot run 3' UTR tests from UCSC on non Unix/Linux machines!
Cannot run 3' UTR tests from UCSC on non Unix/Linux machines!
Cannot run 3' UTR tests from UCSC on non Unix/Linux machines!
Cannot run 3' UTR tests from UCSC on non Unix/Linux machines!
Cannot run 3' UTR tests from UCSC on non Unix/Linux machines!
RUNIT TEST PROTOCOL -- Tue Jul 16 04:31:54 2024
***********************************************
Number of test functions: 8
Number of errors: 0
Number of failures: 0
1 Test Suite :
sitadela RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8
Number of errors: 0
Number of failures: 0
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
68.28 6.93 114.70
sitadela.Rcheck/sitadela-Ex.timings
| name | user | system | elapsed | |
| addAnnotation | 0 | 0 | 0 | |
| addCustomAnnotation | 0 | 0 | 0 | |
| getAnnotation | 3.78 | 0.30 | 9.38 | |
| getInstalledAnnotations | 0 | 0 | 0 | |
| getSeqInfo | 0.14 | 0.03 | 0.39 | |
| getUserAnnotations | 0 | 0 | 0 | |
| getsetDbPath | 0 | 0 | 0 | |
| importCustomAnnotation | 0.01 | 0.00 | 0.01 | |
| loadAnnotation | 0 | 0 | 0 | |
| removeAnnotation | 0 | 0 | 0 | |
| testFuns | 5.22 | 0.30 | 5.97 | |