Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1003/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
iCOBRA 1.34.0 (landing page) Charlotte Soneson
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | 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 iCOBRA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iCOBRA.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: iCOBRA |
Version: 1.34.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iCOBRA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iCOBRA_1.34.0.tar.gz |
StartedAt: 2024-11-19 23:07:28 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 23:12:44 -0500 (Tue, 19 Nov 2024) |
EllapsedTime: 315.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: iCOBRA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iCOBRA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iCOBRA_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/iCOBRA.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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘iCOBRA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘iCOBRA’ version ‘1.34.0’ * package encoding: UTF-8 * 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 ‘iCOBRA’ 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 dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘markdown’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE plot_deviation: no visible binding for global variable ‘method’ plot_fdrcurve: no visible binding for global variable ‘method’ plot_fdrcurve: no visible binding for global variable ‘method2.satis’ plot_fdrcurve: no visible binding for global variable ‘thr’ plot_fpr_tpr: no visible binding for global variable ‘method’ plot_fpr_tpr: no visible binding for global variable ‘thr’ plot_roc_fpc: no visible binding for global variable ‘method’ plot_scatter: no visible binding for global variable ‘OBSERVATION’ plot_scatter: no visible binding for global variable ‘TRUTH’ plot_scatter: no visible binding for global variable ‘fullmethod’ Undefined global functions or variables: OBSERVATION TRUTH fullmethod method method2.satis thr * 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 LazyData ... 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 ‘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-3.20-bioc/meat/iCOBRA.Rcheck/00check.log’ for details.
iCOBRA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL iCOBRA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘iCOBRA’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (iCOBRA)
iCOBRA.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(testthat) > library(iCOBRA) > > test_check("iCOBRA") An object of class "COBRAData" @pval Method1 Method2 Method3 ENSG00000000457 0.01446441 0.008665558 0.003317162 ENSG00000000460 0.95247473 0.927616428 0.974301159 ENSG00000000938 0.74556923 0.632987431 0.639716304 ENSG00000000971 0.72582371 0.568683774 0.610769221 ENSG00000001460 0.64292689 0.629807292 0.613039563 2413 more rows ... @padj Method1 Method2 ENSG00000000457 0.05544853 0.03916508 ENSG00000000460 0.98752284 0.96680023 ENSG00000000938 0.91465571 0.82867282 ENSG00000000971 0.90618247 0.79410144 ENSG00000001460 0.87662457 0.82779499 2413 more rows ... @sval Method1 Method2 ENSG00000000457 0.05544853 0.03916508 ENSG00000000460 0.98752284 0.96680023 ENSG00000000938 0.91465571 0.82867282 ENSG00000000971 0.90618247 0.79410144 ENSG00000001460 0.87662457 0.82779499 2413 more rows ... @score Method1 Method2 Method3 ENSG00000000457 -0.76274305 -0.75783824 -0.743951068 ENSG00000000460 -0.02033394 -0.02096682 -0.007355491 ENSG00000000938 0.10235482 0.10968180 0.113127202 ENSG00000000971 -0.12495998 -0.12090589 -0.112072431 ENSG00000001460 -0.16319682 -0.13257307 -0.149343205 2413 more rows ... @truth status n_isoforms logFC logFC_cat expr ENSG00000000457 0 5 0.0000000 [ 0.00, 0.56) 8.525774 ENSG00000000460 1 10 1.1643146 [ 0.56, 1.54) 5.371661 ENSG00000000938 0 8 0.0000000 [ 0.00, 0.56) 11.543626 ENSG00000000971 0 6 0.0000000 [ 0.00, 0.56) 163.547797 ENSG00000001460 1 13 -0.1033807 [ 0.00, 0.56) 6.874695 expr_cat ENSG00000000457 [ 2.628, 17.148) ENSG00000000460 [ 2.628, 17.148) ENSG00000000938 [ 2.628, 17.148) ENSG00000000971 [ 17.148,3265.406] ENSG00000001460 [ 2.628, 17.148) 3853 more rows ... An object of class "COBRAPerformance" @fdrtpr data frame with 0 columns and 0 rows @fdrtprcurve data frame with 0 columns and 0 rows @fdrnbr data frame with 0 columns and 0 rows @fdrnbrcurve data frame with 0 columns and 0 rows @fsrnbr data frame with 0 columns and 0 rows @fsrnbrcurve data frame with 0 columns and 0 rows @deviation data frame with 0 columns and 0 rows @tpr thr method basemethod meas fullmethod splitval NBR TP FP TN 1 thr0.01 Method1 Method1 __padj Method1_overall overall 508 387 121 1473 2 thr0.01 Method2 Method2 __padj Method2_overall overall 392 308 84 1510 3 thr0.05 Method1 Method1 __padj Method1_overall overall 620 448 172 1422 4 thr0.05 Method2 Method2 __padj Method2_overall overall 565 406 159 1435 5 thr0.1 Method1 Method1 __padj Method1_overall overall 697 478 219 1375 6 thr0.1 Method2 Method2 __padj Method2_overall overall 651 448 203 1391 FN TOT_CALLED DIFF NONDIFF TPR 1 437 2418 842 3016 0.4596200 2 516 2418 842 3016 0.3657957 3 376 2418 842 3016 0.5320665 4 418 2418 842 3016 0.4821853 5 346 2418 842 3016 0.5676960 6 376 2418 842 3016 0.5320665 @fpr data frame with 0 columns and 0 rows @roc data frame with 0 columns and 0 rows @scatter data frame with 0 columns and 0 rows @fpc data frame with 0 columns and 0 rows @overlap data frame with 0 columns and 0 rows @corr data frame with 0 columns and 0 rows @maxsplit [1] 3 @splv [1] "none" @onlyshared [1] FALSE An object of class "COBRAPerformance" @fdrtpr data frame with 0 columns and 0 rows @fdrtprcurve data frame with 0 columns and 0 rows @fdrnbr data frame with 0 columns and 0 rows @fdrnbrcurve data frame with 0 columns and 0 rows @fsrnbr data frame with 0 columns and 0 rows @fsrnbrcurve data frame with 0 columns and 0 rows @deviation data frame with 0 columns and 0 rows @tpr thr method basemethod meas fullmethod 1 thr0.01 Method1 Method1 __padj Method1_expr_cat:[ 0.000, 0.362) 2 thr0.01 Method1 Method1 __padj Method1_expr_cat:[ 0.362, 2.628) 3 thr0.01 Method1 Method1 __padj Method1_expr_cat:[ 2.628, 17.148) 4 thr0.01 Method1 Method1 __padj Method1_expr_cat:[ 17.148,3265.406] 5 thr0.01 Method1 Method1 __padj Method1_overall splitval NBR TP FP TN FN TOT_CALLED DIFF NONDIFF 1 expr_cat:[ 0.000, 0.362) 18 12 6 341 12 371 30 1747 2 expr_cat:[ 0.362, 2.628) 112 100 12 374 175 661 287 406 3 expr_cat:[ 2.628, 17.148) 157 102 55 414 121 692 223 471 4 expr_cat:[ 17.148,3265.406] 221 173 48 344 129 694 302 392 5 overall 508 387 121 1473 437 2418 842 3016 TPR 1 0.4000000 2 0.3484321 3 0.4573991 4 0.5728477 5 0.4596200 25 more rows ... @fpr data frame with 0 columns and 0 rows @roc data frame with 0 columns and 0 rows @scatter data frame with 0 columns and 0 rows @fpc data frame with 0 columns and 0 rows @overlap $[ 0.000, 0.362) Method1 Method2 truth ENSG00000007908 0 0 0 ENSG00000008118 0 0 0 ENSG00000042781 0 0 0 ENSG00000049247 0 0 1 ENSG00000057468 0 0 0 1772 more rows ... $[ 2.628, 17.148) Method1 Method2 truth ENSG00000000457 0 1 0 ENSG00000000460 0 0 1 ENSG00000000938 0 0 0 ENSG00000001460 0 0 1 ENSG00000006555 0 0 1 689 more rows ... $[ 17.148,3265.406] Method1 Method2 truth ENSG00000000971 0 0 0 ENSG00000001461 0 0 0 ENSG00000004455 1 1 0 ENSG00000004487 0 0 1 ENSG00000007923 0 0 0 689 more rows ... $[ 0.362, 2.628) Method1 Method2 truth ENSG00000007933 0 0 0 ENSG00000007968 1 1 0 ENSG00000009724 0 0 0 ENSG00000010932 0 0 1 ENSG00000024526 1 1 1 688 more rows ... $overall Method1 Method2 truth ENSG00000000457 0 1 0 ENSG00000000460 0 0 1 ENSG00000000938 0 0 0 ENSG00000000971 0 0 0 ENSG00000001460 0 0 1 3853 more rows ... @corr data frame with 0 columns and 0 rows @maxsplit [1] 4 @splv [1] "expr_cat" @onlyshared [1] FALSE An object of class "COBRAPlot" @plotcolors Method1 Method2 "#00ACFC" "#8B93FF" truth Method1_expr_cat:[ 0.000, 0.362) "#FF65AC" "#F8766D" Method2_expr_cat:[ 0.000, 0.362) "#E18A00" 58 more elements ... @facetted [1] FALSE @fdrtpr data frame with 0 columns and 0 rows @fdrtprcurve data frame with 0 columns and 0 rows @fdrnbr data frame with 0 columns and 0 rows @fdrnbrcurve data frame with 0 columns and 0 rows @fsrnbr data frame with 0 columns and 0 rows @fsrnbrcurve data frame with 0 columns and 0 rows @deviation data frame with 0 columns and 0 rows @tpr thr method basemethod meas fullmethod 1 thr0.01 Method1 Method1 __padj Method1_expr_cat:[ 0.000, 0.362) 2 thr0.01 Method1 Method1 __padj Method1_expr_cat:[ 0.362, 2.628) 3 thr0.01 Method1 Method1 __padj Method1_expr_cat:[ 2.628, 17.148) 4 thr0.01 Method1 Method1 __padj Method1_expr_cat:[ 17.148,3265.406] 5 thr0.01 Method1 Method1 __padj Method1_overall splitval NBR TP FP TN FN TOT_CALLED DIFF NONDIFF 1 expr_cat:[ 0.000, 0.362) 18 12 6 341 12 371 30 1747 2 expr_cat:[ 0.362, 2.628) 112 100 12 374 175 661 287 406 3 expr_cat:[ 2.628, 17.148) 157 102 55 414 121 692 223 471 4 expr_cat:[ 17.148,3265.406] 221 173 48 344 129 694 302 392 5 overall 508 387 121 1473 437 2418 842 3016 TPR num_method 1 0.4000000 1 2 0.3484321 2 3 0.4573991 3 4 0.5728477 4 5 0.4596200 5 25 more rows ... @fpr data frame with 0 columns and 0 rows @roc data frame with 0 columns and 0 rows @scatter data frame with 0 columns and 0 rows @fpc data frame with 0 columns and 0 rows @overlap $[ 0.000, 0.362) Method1 Method2 truth ENSG00000007908 0 0 0 ENSG00000008118 0 0 0 ENSG00000042781 0 0 0 ENSG00000049247 0 0 1 ENSG00000057468 0 0 0 1772 more rows ... $[ 2.628, 17.148) Method1 Method2 truth ENSG00000000457 0 1 0 ENSG00000000460 0 0 1 ENSG00000000938 0 0 0 ENSG00000001460 0 0 1 ENSG00000006555 0 0 1 689 more rows ... $[ 17.148,3265.406] Method1 Method2 truth ENSG00000000971 0 0 0 ENSG00000001461 0 0 0 ENSG00000004455 1 1 0 ENSG00000004487 0 0 1 ENSG00000007923 0 0 0 689 more rows ... $[ 0.362, 2.628) Method1 Method2 truth ENSG00000007933 0 0 0 ENSG00000007968 1 1 0 ENSG00000009724 0 0 0 ENSG00000010932 0 0 1 ENSG00000024526 1 1 1 688 more rows ... $overall Method1 Method2 truth ENSG00000000457 0 1 0 ENSG00000000460 0 0 1 ENSG00000000938 0 0 0 ENSG00000000971 0 0 0 ENSG00000001460 0 0 1 3853 more rows ... @corr data frame with 0 columns and 0 rows @maxsplit [1] 4 @splv [1] "expr_cat" @onlyshared [1] FALSE [ FAIL 0 | WARN 0 | SKIP 0 | PASS 408 ] > > proc.time() user system elapsed 33.356 0.926 34.390
iCOBRA.Rcheck/iCOBRA-Ex.timings
name | user | system | elapsed | |
COBRAData | 0.004 | 0.001 | 0.005 | |
COBRAPerformance | 0.002 | 0.001 | 0.004 | |
COBRAPlot | 0.001 | 0.000 | 0.001 | |
COBRAapp | 0.346 | 0.031 | 0.382 | |
Extract | 0.143 | 0.020 | 0.163 | |
basemethods | 0.180 | 0.006 | 0.185 | |
calculate_adjp | 0.010 | 0.002 | 0.011 | |
calculate_performance | 0.395 | 0.015 | 0.411 | |
coerce | 0.059 | 0.005 | 0.064 | |
corr | 0.019 | 0.002 | 0.020 | |
deviation | 0.281 | 0.004 | 0.286 | |
facetted | 0.058 | 0.005 | 0.064 | |
fdrnbr | 0.046 | 0.003 | 0.047 | |
fdrnbrcurve | 0.189 | 0.009 | 0.198 | |
fdrtpr | 0.048 | 0.003 | 0.051 | |
fdrtprcurve | 0.198 | 0.008 | 0.207 | |
fpc | 0.177 | 0.003 | 0.180 | |
fpr | 0.042 | 0.001 | 0.044 | |
fsrnbr | 0.027 | 0.001 | 0.029 | |
fsrnbrcurve | 0.500 | 0.059 | 0.560 | |
maxsplit | 0.150 | 0.008 | 0.159 | |
onlyshared | 0.047 | 0.003 | 0.049 | |
overlap | 0.009 | 0.002 | 0.010 | |
padj | 0.005 | 0.001 | 0.007 | |
plot_corr | 0.214 | 0.008 | 0.223 | |
plot_deviation | 0.748 | 0.015 | 0.764 | |
plot_fdrnbrcurve | 0.610 | 0.009 | 0.621 | |
plot_fdrtprcurve | 0.503 | 0.008 | 0.513 | |
plot_fpc | 0.342 | 0.004 | 0.347 | |
plot_fpr | 0.174 | 0.004 | 0.179 | |
plot_fsrnbrcurve | 0.744 | 0.046 | 0.794 | |
plot_overlap | 0.025 | 0.001 | 0.027 | |
plot_roc | 0.331 | 0.005 | 0.337 | |
plot_scatter | 0.530 | 0.010 | 0.542 | |
plot_tpr | 0.262 | 0.003 | 0.265 | |
plot_upset | 1.182 | 0.015 | 1.200 | |
plotcolors | 0.051 | 0.001 | 0.054 | |
prepare_data_for_plot | 0.407 | 0.009 | 0.417 | |
pval | 0.006 | 0.002 | 0.006 | |
reorder_levels | 0.046 | 0.004 | 0.050 | |
roc | 0.162 | 0.001 | 0.163 | |
scatter | 0.262 | 0.002 | 0.263 | |
score | 0.005 | 0.000 | 0.006 | |
splv | 0.130 | 0.004 | 0.134 | |
stratiflevels | 0.155 | 0.006 | 0.161 | |
sval | 0.005 | 0.001 | 0.005 | |
tpr | 0.045 | 0.004 | 0.049 | |
truth | 0.005 | 0.001 | 0.006 | |
update_cobradata | 0.002 | 0.000 | 0.001 | |
update_cobraperformance | 0.035 | 0.000 | 0.035 | |