| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 12:30:49 -0400 (Tue, 09 Apr 2019).
| Package 211/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CATALYST 1.7.7 Helena L. Crowell
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: CATALYST |
| Version: 1.7.7 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CATALYST.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CATALYST_1.7.7.tar.gz |
| StartedAt: 2019-04-09 01:32:59 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:48:11 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 911.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: CATALYST.Rcheck |
| Warnings: NA |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CATALYST.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CATALYST_1.7.7.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/CATALYST.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CATALYST/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CATALYST' version '1.7.7'
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'CATALYST' 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotClusterHeatmap,daFrame : <anonymous>: no visible binding for global
variable 'cluster_id'
Undefined global functions or variables:
cluster_id
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
runDR 27.90 0.14 30.06
plotClusterExprs 20.66 0.42 21.08
plotClusterHeatmap 13.31 0.28 13.59
plotMedExprs 13.36 0.05 13.40
plotYields 12.42 0.22 12.47
plotMahal 11.17 0.00 11.18
outFCS 10.14 0.02 10.15
normCytof 9.36 0.08 9.46
plotAbundances 9.06 0.08 9.14
plotEvents 8.97 0.00 8.97
mergeClusters 8.39 0.01 8.40
applyCutoffs 8.38 0.00 8.38
outFrames 7.92 0.01 7.94
plotDR 7.76 0.06 7.82
plotDiffHeatmap 7.14 0.13 7.24
plotCodes 7.15 0.02 7.17
adaptSpillmat 6.65 0.47 7.15
estCutoffs 6.83 0.08 12.95
extractClusters 6.78 0.08 6.96
assignPrelim 6.60 0.02 6.61
plotSpillmat 6.52 0.02 6.53
dbFrame-methods 6.49 0.00 6.49
daFrame-methods 6.20 0.08 6.28
cluster 6.12 0.04 6.17
filter 5.97 0.01 5.98
plotExprs 5.51 0.03 5.55
computeSpillmat 5.23 0.05 5.28
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
runDR 30.61 0.11 30.81
plotClusterExprs 16.80 0.12 16.92
plotClusterHeatmap 11.56 0.06 11.63
plotMahal 11.51 0.03 11.55
plotMedExprs 10.78 0.03 10.81
plotDiffHeatmap 10.44 0.14 10.56
plotYields 9.47 0.13 9.56
plotEvents 8.91 0.00 8.91
applyCutoffs 8.36 0.01 8.38
estCutoffs 7.83 0.06 7.90
computeSpillmat 7.71 0.08 7.78
outFCS 7.69 0.00 7.69
dbFrame-methods 7.11 0.00 7.11
plotAbundances 6.95 0.00 6.95
outFrames 6.88 0.00 6.88
assignPrelim 6.75 0.02 6.77
adaptSpillmat 6.46 0.05 6.50
normCytof 6.34 0.04 6.37
mergeClusters 6.19 0.00 6.19
daFrame-methods 6.11 0.05 6.16
plotCodes 5.78 0.05 5.82
plotDR 5.73 0.00 5.74
plotSpillmat 5.48 0.03 5.52
filter 5.34 0.00 5.34
plotExprs 5.14 0.03 5.19
cluster 5.08 0.01 5.09
compCytof 5.04 0.03 5.08
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
invokeRestart("muffleWarning")
})
5: eval_bare(get_expr(quo), get_env(quo))
6: runDR(y, "PCA", i, use_dimred = "MDS")
7: runDR(y, "PCA", i, use_dimred = "MDS")
8: .local(x, ...)
9: fun(y, exprs_values = "exprs", feature_set = cols_to_use, ...)
10: fun(y, exprs_values = "exprs", feature_set = cols_to_use, ...)
== testthat results ===========================================================
OK: 85 SKIPPED: 0 FAILED: 1
1. Error: throw warning when 'use_dimred' is supplied to PCA (@test_runDR.R#43)
Error: testthat unit tests failed
Execution halted
** running tests for arch 'x64' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
invokeRestart("muffleWarning")
})
5: eval_bare(get_expr(quo), get_env(quo))
6: runDR(y, "PCA", i, use_dimred = "MDS")
7: runDR(y, "PCA", i, use_dimred = "MDS")
8: .local(x, ...)
9: fun(y, exprs_values = "exprs", feature_set = cols_to_use, ...)
10: fun(y, exprs_values = "exprs", feature_set = cols_to_use, ...)
== testthat results ===========================================================
OK: 85 SKIPPED: 0 FAILED: 1
1. Error: throw warning when 'use_dimred' is supplied to PCA (@test_runDR.R#43)
Error: testthat unit tests failed
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/CATALYST.Rcheck/00check.log'
for details.
CATALYST.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/CATALYST_1.7.7.tar.gz && rm -rf CATALYST.buildbin-libdir && mkdir CATALYST.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CATALYST.buildbin-libdir CATALYST_1.7.7.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CATALYST_1.7.7.zip && rm CATALYST_1.7.7.tar.gz CATALYST_1.7.7.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
85 3587k 85 3072k 0 0 22.1M 0 --:--:-- --:--:-- --:--:-- 23.2M
100 3587k 100 3587k 0 0 18.0M 0 --:--:-- --:--:-- --:--:-- 18.6M
install for i386
* installing *source* package 'CATALYST' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'filter' in package 'CATALYST'
** help
*** installing help indices
converting help for package 'CATALYST'
finding HTML links ... done
adaptSpillmat html
applyCutoffs html
assignPrelim html
finding level-2 HTML links ... done
cluster html
compCytof html
computeSpillmat html
concatFCS html
daFrame-class html
daFrame-methods html
data html
dbFrame-class html
dbFrame-methods html
estCutoffs html
extractClusters html
filter html
guessPanel html
launchGUI html
mergeClusters html
normCytof html
outFCS html
outFrames html
plotAbundances html
plotClusterExprs html
plotClusterHeatmap html
plotCodes html
plotCounts html
plotDR html
plotDiffHeatmap html
plotEvents html
plotExprHeatmap html
plotExprs html
plotMDS html
plotMahal html
plotMedExprs html
plotNRS html
plotSpillmat html
plotYields html
runDR html
** 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
install for x64
* installing *source* package 'CATALYST' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CATALYST' as CATALYST_1.7.7.zip
* DONE (CATALYST)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'CATALYST' successfully unpacked and MD5 sums checked
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CATALYST.Rcheck/tests_i386/testthat.Rout.fail
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
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(CATALYST)
Attaching package: 'CATALYST'
The following object is masked from 'package:stats':
filter
>
> test_check("CATALYST")
-- 1. Error: throw warning when 'use_dimred' is supplied to PCA (@test_runDR.R#4
unused argument (use_dimred = "MDS")
1: expect_warning(runDR(y, "PCA", i, use_dimred = "MDS")) at testthat/test_runDR.R:43
2: quasi_capture(enquo(object), capture_warnings, label = label)
3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
4: withCallingHandlers(code, warning = function(condition) {
out$push(condition)
invokeRestart("muffleWarning")
})
5: eval_bare(get_expr(quo), get_env(quo))
6: runDR(y, "PCA", i, use_dimred = "MDS")
7: runDR(y, "PCA", i, use_dimred = "MDS")
8: .local(x, ...)
9: fun(y, exprs_values = "exprs", feature_set = cols_to_use, ...)
10: fun(y, exprs_values = "exprs", feature_set = cols_to_use, ...)
== testthat results ===========================================================
OK: 85 SKIPPED: 0 FAILED: 1
1. Error: throw warning when 'use_dimred' is supplied to PCA (@test_runDR.R#43)
Error: testthat unit tests failed
Execution halted
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CATALYST.Rcheck/tests_x64/testthat.Rout.fail
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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(CATALYST)
Attaching package: 'CATALYST'
The following object is masked from 'package:stats':
filter
>
> test_check("CATALYST")
-- 1. Error: throw warning when 'use_dimred' is supplied to PCA (@test_runDR.R#4
unused argument (use_dimred = "MDS")
1: expect_warning(runDR(y, "PCA", i, use_dimred = "MDS")) at testthat/test_runDR.R:43
2: quasi_capture(enquo(object), capture_warnings, label = label)
3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
4: withCallingHandlers(code, warning = function(condition) {
out$push(condition)
invokeRestart("muffleWarning")
})
5: eval_bare(get_expr(quo), get_env(quo))
6: runDR(y, "PCA", i, use_dimred = "MDS")
7: runDR(y, "PCA", i, use_dimred = "MDS")
8: .local(x, ...)
9: fun(y, exprs_values = "exprs", feature_set = cols_to_use, ...)
10: fun(y, exprs_values = "exprs", feature_set = cols_to_use, ...)
== testthat results ===========================================================
OK: 85 SKIPPED: 0 FAILED: 1
1. Error: throw warning when 'use_dimred' is supplied to PCA (@test_runDR.R#43)
Error: testthat unit tests failed
Execution halted
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CATALYST.Rcheck/examples_i386/CATALYST-Ex.timings
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CATALYST.Rcheck/examples_x64/CATALYST-Ex.timings
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