Steve Lianoglou
| Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/sparrow |
| git_branch: RELEASE_3_19 |
| git_last_commit: d592783 |
| git_last_commit_date: 2024-05-06 17:21:11 -0400 (Mon, 06 May 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-07-12 17:41 -0400 (Fri, 12 Jul 2024).
| 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" | 4741 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
| 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 2024/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sparrow 1.10.1 (landing page) Steve Lianoglou
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.10.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sparrow.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sparrow_1.10.1.tar.gz |
| StartedAt: 2024-07-11 12:10:45 -0400 (Thu, 11 Jul 2024) |
| EndedAt: 2024-07-11 12:33:14 -0400 (Thu, 11 Jul 2024) |
| EllapsedTime: 1348.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sparrow.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sparrow.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sparrow_1.10.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/sparrow.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sparrow/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sparrow’ version ‘1.10.1’
* 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 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 ... 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 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 16.053 0.612 19.567
seas 12.839 0.385 15.750
scoreSingleSamples 10.346 0.417 12.460
annotateGeneSetMembership 8.628 0.169 10.584
SparrowResult-utilities 8.140 0.280 10.069
geneSetsStats 8.105 0.164 9.510
geneSetSummaryByGenes 7.094 0.272 8.950
logFC 6.677 0.199 8.003
eigenWeightedMean 6.449 0.134 7.790
calculateIndividualLogFC 4.648 0.077 5.701
volcanoPlot 4.122 0.213 5.027
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc/meat/sparrow.Rcheck/00check.log’
for details.
sparrow.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sparrow ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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 1489 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-MultiGSEAResult.R:3:1'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 1489 ]
>
> ## 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
646.310 30.421 742.204
sparrow.Rcheck/sparrow-Ex.timings
| name | user | system | elapsed | |
| GeneSetDb-class | 0.334 | 0.012 | 0.415 | |
| SparrowResult-utilities | 8.140 | 0.280 | 10.069 | |
| addGeneSetMetadata | 0.127 | 0.003 | 0.158 | |
| annotateGeneSetMembership | 8.628 | 0.169 | 10.584 | |
| calculateIndividualLogFC | 4.648 | 0.077 | 5.701 | |
| collectionMetadata | 0.148 | 0.003 | 0.180 | |
| combine-GeneSetDb-GeneSetDb-method | 0.167 | 0.005 | 0.205 | |
| combine-SparrowResult-SparrowResult-method | 0.217 | 0.007 | 0.272 | |
| conform | 0.847 | 0.027 | 1.041 | |
| conversion | 1.191 | 0.037 | 1.491 | |
| convertIdentifiers | 0.320 | 0.007 | 0.397 | |
| corplot | 0.172 | 0.008 | 0.217 | |
| eigenWeightedMean | 6.449 | 0.134 | 7.790 | |
| examples | 0.631 | 0.202 | 0.987 | |
| failWith | 0.000 | 0.001 | 0.001 | |
| featureIdMap | 0.828 | 0.016 | 0.987 | |
| featureIds | 0.913 | 0.034 | 1.155 | |
| geneSet | 0.176 | 0.008 | 0.220 | |
| geneSetCollectionURLfunction | 0.113 | 0.004 | 0.143 | |
| geneSetSummaryByGenes | 7.094 | 0.272 | 8.950 | |
| geneSets | 0.132 | 0.014 | 0.199 | |
| geneSetsStats | 8.105 | 0.164 | 9.510 | |
| getKeggCollection | 0 | 0 | 0 | |
| getMSigCollection | 0 | 0 | 0 | |
| getPantherCollection | 0 | 0 | 0 | |
| getReactomeCollection | 0 | 0 | 0 | |
| goseq | 16.053 | 0.612 | 19.567 | |
| gsdScore | 1.953 | 0.052 | 2.319 | |
| gskey | 0.006 | 0.002 | 0.007 | |
| hasGeneSet | 0.114 | 0.002 | 0.139 | |
| hasGeneSetCollection | 0.108 | 0.002 | 0.127 | |
| incidenceMatrix | 2.375 | 0.046 | 2.837 | |
| iplot | 3.597 | 0.283 | 4.719 | |
| is.active | 0.713 | 0.102 | 0.956 | |
| logFC | 6.677 | 0.199 | 8.003 | |
| mgheatmap | 0.000 | 0.001 | 0.001 | |
| mgheatmap2 | 0 | 0 | 0 | |
| msg | 0.001 | 0.001 | 0.001 | |
| ora | 0.460 | 0.028 | 0.598 | |
| p.matrix | 0.164 | 0.004 | 0.188 | |
| randomGeneSetDb | 0.165 | 0.013 | 0.196 | |
| renameCollections | 0.178 | 0.005 | 0.201 | |
| renameRows | 0.675 | 0.012 | 0.763 | |
| results | 0.248 | 0.021 | 0.301 | |
| scale_rows | 0.007 | 0.001 | 0.009 | |
| scoreSingleSamples | 10.346 | 0.417 | 12.460 | |
| seas | 12.839 | 0.385 | 15.750 | |
| sparrow_methods | 0.007 | 0.003 | 0.013 | |
| species_info | 0.013 | 0.006 | 0.023 | |
| subset.GeneSetDb | 0.172 | 0.002 | 0.203 | |
| subsetByFeatures | 0.152 | 0.004 | 0.183 | |
| validateInputs | 0.319 | 0.029 | 0.413 | |
| volcanoPlot | 4.122 | 0.213 | 5.027 | |
| volcanoStatsTable | 0.122 | 0.003 | 0.146 | |
| zScore | 1.783 | 0.043 | 2.107 | |