Steve Lianoglou
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/sparrow |
| git_branch: devel |
| git_last_commit: 007735d |
| git_last_commit_date: 2024-02-02 18:23:42 -0400 (Fri, 02 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:37:07 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 1997/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sparrow 1.9.1 (landing page) Steve Lianoglou
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the sparrow package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sparrow.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: sparrow |
| Version: 1.9.1 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings sparrow_1.9.1.tar.gz |
| StartedAt: 2024-03-28 02:54:38 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 03:06:21 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 702.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sparrow.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings sparrow_1.9.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/sparrow.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* 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 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘sparrow/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sparrow’ version ‘1.9.1’
* 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 ‘sparrow’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 whether startup messages can be suppressed ... 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 ... NOTE
geneSetsStats: no visible binding for global variable ‘direction’
Undefined global functions or variables:
direction
* checking Rd files ... NOTE
checkRd: (-1) convertIdentifiers.Rd:118: Lost braces; missing escapes or markup?
118 | rely on the {babelgene} package for the conversion, so you will have to
| ^
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
goseq 7.755 0.192 7.022
geneSetsStats 5.456 0.071 3.781
seas 5.224 0.144 4.435
SparrowResult-utilities 4.884 0.179 4.175
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/sparrow.Rcheck/00check.log’
for details.
sparrow.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL sparrow ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘sparrow’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (sparrow)
sparrow.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-03-18 r86148) -- "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.
> library("sparrow")
> library("testthat")
> library("data.table")
> library("dplyr")
Attaching package: 'dplyr'
The following objects are masked from 'package:data.table':
between, first, last
The following object is masked from 'package:testthat':
matches
The following object is masked from 'package:sparrow':
combine
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
>
> test_check("sparrow")
Attaching package: 'magrittr'
The following objects are masked from 'package:testthat':
equals, is_less_than, not
Estimating GSVA scores for 76 gene sets.
Estimating ECDFs with Gaussian kernels
|
| | 0%
|
|= | 1%
|
|== | 3%
|
|=== | 4%
|
|==== | 5%
|
|===== | 7%
|
|====== | 8%
|
|====== | 9%
|
|======= | 11%
|
|======== | 12%
|
|========= | 13%
|
|========== | 14%
|
|=========== | 16%
|
|============ | 17%
|
|============= | 18%
|
|============== | 20%
|
|=============== | 21%
|
|================ | 22%
|
|================= | 24%
|
|================== | 25%
|
|================== | 26%
|
|=================== | 28%
|
|==================== | 29%
|
|===================== | 30%
|
|====================== | 32%
|
|======================= | 33%
|
|======================== | 34%
|
|========================= | 36%
|
|========================== | 37%
|
|=========================== | 38%
|
|============================ | 39%
|
|============================= | 41%
|
|============================= | 42%
|
|============================== | 43%
|
|=============================== | 45%
|
|================================ | 46%
|
|================================= | 47%
|
|================================== | 49%
|
|=================================== | 50%
|
|==================================== | 51%
|
|===================================== | 53%
|
|====================================== | 54%
|
|======================================= | 55%
|
|======================================== | 57%
|
|========================================= | 58%
|
|========================================= | 59%
|
|========================================== | 61%
|
|=========================================== | 62%
|
|============================================ | 63%
|
|============================================= | 64%
|
|============================================== | 66%
|
|=============================================== | 67%
|
|================================================ | 68%
|
|================================================= | 70%
|
|================================================== | 71%
|
|=================================================== | 72%
|
|==================================================== | 74%
|
|==================================================== | 75%
|
|===================================================== | 76%
|
|====================================================== | 78%
|
|======================================================= | 79%
|
|======================================================== | 80%
|
|========================================================= | 82%
|
|========================================================== | 83%
|
|=========================================================== | 84%
|
|============================================================ | 86%
|
|============================================================= | 87%
|
|============================================================== | 88%
|
|=============================================================== | 89%
|
|================================================================ | 91%
|
|================================================================ | 92%
|
|================================================================= | 93%
|
|================================================================== | 95%
|
|=================================================================== | 96%
|
|==================================================================== | 97%
|
|===================================================================== | 99%
|
|======================================================================| 100%
Estimating PLAGE scores for 76 gene sets.
|
| | 0%
|
|= | 1%
|
|== | 3%
|
|=== | 4%
|
|==== | 5%
|
|===== | 7%
|
|====== | 8%
|
|====== | 9%
|
|======= | 11%
|
|======== | 12%
|
|========= | 13%
|
|========== | 14%
|
|=========== | 16%
|
|============ | 17%
|
|============= | 18%
|
|============== | 20%
|
|=============== | 21%
|
|================ | 22%
|
|================= | 24%
|
|================== | 25%
|
|================== | 26%
|
|=================== | 28%
|
|==================== | 29%
|
|===================== | 30%
|
|====================== | 32%
|
|======================= | 33%
|
|======================== | 34%
|
|========================= | 36%
|
|========================== | 37%
|
|=========================== | 38%
|
|============================ | 39%
|
|============================= | 41%
|
|============================= | 42%
|
|============================== | 43%
|
|=============================== | 45%
|
|================================ | 46%
|
|================================= | 47%
|
|================================== | 49%
|
|=================================== | 50%
|
|==================================== | 51%
|
|===================================== | 53%
|
|====================================== | 54%
|
|======================================= | 55%
|
|======================================== | 57%
|
|========================================= | 58%
|
|========================================= | 59%
|
|========================================== | 61%
|
|=========================================== | 62%
|
|============================================ | 63%
|
|============================================= | 64%
|
|============================================== | 66%
|
|=============================================== | 67%
|
|================================================ | 68%
|
|================================================= | 70%
|
|================================================== | 71%
|
|=================================================== | 72%
|
|==================================================== | 74%
|
|==================================================== | 75%
|
|===================================================== | 76%
|
|====================================================== | 78%
|
|======================================================= | 79%
|
|======================================================== | 80%
|
|========================================================= | 82%
|
|========================================================== | 83%
|
|=========================================================== | 84%
|
|============================================================ | 86%
|
|============================================================= | 87%
|
|============================================================== | 88%
|
|=============================================================== | 89%
|
|================================================================ | 91%
|
|================================================================ | 92%
|
|================================================================= | 93%
|
|================================================================== | 95%
|
|=================================================================== | 96%
|
|==================================================================== | 97%
|
|===================================================================== | 99%
|
|======================================================================| 100%
Estimating ssGSEA scores for 76 gene sets.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
|
| | 0%
|
|==== | 6%
|
|======== | 11%
|
|============ | 17%
|
|================ | 22%
|
|=================== | 28%
|
|======================= | 33%
|
|=========================== | 39%
|
|=============================== | 44%
|
|=================================== | 50%
|
|======================================= | 56%
|
|=========================================== | 61%
|
|=============================================== | 67%
|
|=================================================== | 72%
|
|====================================================== | 78%
|
|========================================================== | 83%
|
|============================================================== | 89%
|
|================================================================== | 94%
|
|======================================================================| 100%
[1] "Normalizing..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 1491 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-MultiGSEAResult.R:3:1'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 1491 ]
>
> ## Remove temporary files that were generated
> test.dir <- system.file('tests', package = "sparrow")
> pdfs <- dir(test.dir, "\\.pdf$", full.names=TRUE)
> if (length(pdfs)) {
+ unlink(pdfs)
+ }
>
>
> proc.time()
user system elapsed
331.799 15.448 299.947
sparrow.Rcheck/sparrow-Ex.timings
| name | user | system | elapsed | |
| GeneSetDb-class | 0.091 | 0.000 | 0.074 | |
| SparrowResult-utilities | 4.884 | 0.179 | 4.175 | |
| addGeneSetMetadata | 0.085 | 0.000 | 0.060 | |
| annotateGeneSetMembership | 4.480 | 0.047 | 3.649 | |
| calculateIndividualLogFC | 1.412 | 0.036 | 1.448 | |
| collectionMetadata | 0.087 | 0.004 | 0.066 | |
| combine-GeneSetDb-GeneSetDb-method | 0.128 | 0.000 | 0.081 | |
| combine-SparrowResult-SparrowResult-method | 0.116 | 0.004 | 0.118 | |
| conform | 0.416 | 0.000 | 0.392 | |
| conversion | 0.675 | 0.040 | 0.603 | |
| convertIdentifiers | 0.244 | 0.012 | 0.165 | |
| corplot | 0.091 | 0.004 | 0.095 | |
| eigenWeightedMean | 3.346 | 0.152 | 3.448 | |
| examples | 0.273 | 0.072 | 0.346 | |
| failWith | 0.000 | 0.000 | 0.001 | |
| featureIdMap | 0.422 | 0.000 | 0.396 | |
| featureIds | 0.463 | 0.004 | 0.428 | |
| geneSet | 0.109 | 0.000 | 0.074 | |
| geneSetCollectionURLfunction | 0.081 | 0.000 | 0.056 | |
| geneSetSummaryByGenes | 3.999 | 0.071 | 3.013 | |
| geneSets | 0.083 | 0.001 | 0.054 | |
| geneSetsStats | 5.456 | 0.071 | 3.781 | |
| getKeggCollection | 0 | 0 | 0 | |
| getMSigCollection | 0.000 | 0.000 | 0.001 | |
| getPantherCollection | 0 | 0 | 0 | |
| getReactomeCollection | 0 | 0 | 0 | |
| goseq | 7.755 | 0.192 | 7.022 | |
| gsdScore | 1.950 | 0.104 | 2.003 | |
| gskey | 0.003 | 0.000 | 0.003 | |
| hasGeneSet | 0.079 | 0.000 | 0.054 | |
| hasGeneSetCollection | 0.073 | 0.004 | 0.052 | |
| incidenceMatrix | 1.033 | 0.000 | 1.008 | |
| iplot | 1.169 | 0.080 | 1.199 | |
| is.active | 0.371 | 0.012 | 0.359 | |
| logFC | 3.581 | 0.032 | 2.700 | |
| mgheatmap | 0 | 0 | 0 | |
| mgheatmap2 | 0 | 0 | 0 | |
| msg | 0.001 | 0.000 | 0.001 | |
| ora | 0.283 | 0.016 | 0.293 | |
| p.matrix | 0.087 | 0.000 | 0.087 | |
| randomGeneSetDb | 0.082 | 0.000 | 0.077 | |
| renameCollections | 0.109 | 0.000 | 0.075 | |
| renameRows | 0.450 | 0.004 | 0.450 | |
| results | 0.098 | 0.004 | 0.102 | |
| scale_rows | 0.005 | 0.000 | 0.004 | |
| scoreSingleSamples | 4.423 | 0.200 | 4.523 | |
| seas | 5.224 | 0.144 | 4.435 | |
| sparrow_methods | 0.001 | 0.003 | 0.003 | |
| species_info | 0.006 | 0.000 | 0.007 | |
| subset.GeneSetDb | 0.090 | 0.004 | 0.064 | |
| subsetByFeatures | 0.121 | 0.004 | 0.075 | |
| validateInputs | 0.326 | 0.012 | 0.309 | |
| volcanoPlot | 1.790 | 0.044 | 1.834 | |
| volcanoStatsTable | 0.063 | 0.000 | 0.063 | |
| zScore | 0.854 | 0.004 | 0.804 | |