Argiris Sakellariou
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/mAPKL |
| git_branch: RELEASE_3_13 |
| git_last_commit: 3f87c86 |
| git_last_commit_date: 2021-05-19 12:10:36 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:10 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the mAPKL package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mAPKL.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1029/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mAPKL 1.22.0 (landing page) Argiris Sakellariou
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: mAPKL |
| Version: 1.22.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mAPKL.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings mAPKL_1.22.0.tar.gz |
| StartedAt: 2021-10-15 01:20:35 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 01:39:42 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 1146.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: mAPKL.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mAPKL.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings mAPKL_1.22.0.tar.gz
###
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##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/mAPKL.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mAPKL/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mAPKL' version '1.22.0'
* 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 'mAPKL' 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
mAPKL 110.89 0.54 111.44
netwAttr 109.92 0.33 110.25
classification 107.95 1.46 109.40
preprocess 26.24 0.22 26.45
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
classification 116.80 0.51 117.31
mAPKL 107.23 0.33 107.56
netwAttr 104.47 0.25 104.73
preprocess 24.12 0.19 24.32
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.R'
OK
* 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: OK
mAPKL.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/mAPKL_1.22.0.tar.gz && rm -rf mAPKL.buildbin-libdir && mkdir mAPKL.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mAPKL.buildbin-libdir mAPKL_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL mAPKL_1.22.0.zip && rm mAPKL_1.22.0.tar.gz mAPKL_1.22.0.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
8 4866k 8 402k 0 0 818k 0 0:00:05 --:--:-- 0:00:05 818k
56 4866k 56 2742k 0 0 1894k 0 0:00:02 0:00:01 0:00:01 1893k
100 4866k 100 4866k 0 0 2265k 0 0:00:02 0:00:02 --:--:-- 2266k
install for i386
* installing *source* package 'mAPKL' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'mAPKL'
finding HTML links ... done
Annot-class html
Classify-class html
DataLD-class html
NetAttr-class html
annotate html
classification html
loadFiles html
mAPKL-package html
mAPKL html
mAPKLRes-class html
metrics html
netwAttr html
preprocess html
probes2pathways html
report html
sampling html
*** 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
install for x64
* installing *source* package 'mAPKL' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mAPKL' as mAPKL_1.22.0.zip
* DONE (mAPKL)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'mAPKL' successfully unpacked and MD5 sums checked
|
mAPKL.Rcheck/tests_i386/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.
> BiocGenerics:::testPackage("mAPKL")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Assign 60% as train data and 40% as test data
Saving density graph for breast$trainData in C:/Users/biocbuild/bbs-3.13-bioc/meat/mAPKL.Rcheck/tests_i386
Saving density graph for breast$testData in C:/Users/biocbuild/bbs-3.13-bioc/meat/mAPKL.Rcheck/tests_i386
b=10 b=20 b=30 b=40 b=50 b=60 b=70 b=80 b=90 b=100
b=110 b=120 b=130 b=140 b=150 b=160 b=170 b=180 b=190 b=200
b=210 b=220 b=230 b=240 b=250 b=260 b=270 b=280 b=290 b=300
b=310 b=320 b=330 b=340 b=350 b=360 b=370 b=380 b=390 b=400
b=410 b=420 b=430 b=440 b=450 b=460 b=470 b=480 b=490 b=500
b=510 b=520 b=530 b=540 b=550 b=560 b=570 b=580 b=590 b=600
b=610 b=620 b=630 b=640 b=650 b=660 b=670 b=680 b=690 b=700
b=710 b=720 b=730 b=740 b=750 b=760 b=770 b=780 b=790 b=800
b=810 b=820 b=830 b=840 b=850 b=860 b=870 b=880 b=890 b=900
b=910 b=920 b=930 b=940 b=950 b=960 b=970 b=980 b=990 b=1000
Please wait! The (KL) cluster indexing may take several minutes...
Asking for 22 number of clusters
fc according to limma
Loading required package: hgu133plus2.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: org.Hs.eg.db
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Negative samples: 8
Positive samples: 4
TN=6
FP=2
TP=3
FN=1
AUC=0.75
Accuracy=75.00
MCC=0.48
Specificity=0.75
Sensitivity=0.75
Assign 60% as train data and 40% as test data
RUNIT TEST PROTOCOL -- Fri Oct 15 01:37:29 2021
***********************************************
Number of test functions: 3
Number of errors: 0
Number of failures: 0
1 Test Suite :
mAPKL RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3
Number of errors: 0
Number of failures: 0
Warning messages:
1: In xtfrm.data.frame(x) : cannot xtfrm data frames
2: In xtfrm.data.frame(x) : cannot xtfrm data frames
3: In xtfrm.data.frame(x) : cannot xtfrm data frames
4: In .local(s, x = x, ...) : algorithm did not converge; turn on details
and call plot() to monitor net similarity. Consider
increasing 'maxits' and 'convits', and, if oscillations occur
also increasing damping factor 'lam'.
5: In .local(s, x = x, ...) : algorithm did not converge; turn on details
and call plot() to monitor net similarity. Consider
increasing 'maxits' and 'convits', and, if oscillations occur
also increasing damping factor 'lam'.
6: In .local(s, x = x, ...) : algorithm did not converge; turn on details
and call plot() to monitor net similarity. Consider
increasing 'maxits' and 'convits', and, if oscillations occur
also increasing damping factor 'lam'.
7: In .local(s, x = x, ...) : algorithm did not converge; turn on details
and call plot() to monitor net similarity. Consider
increasing 'maxits' and 'convits', and, if oscillations occur
also increasing damping factor 'lam'.
8: In xtfrm.data.frame(x) : cannot xtfrm data frames
9: In xtfrm.data.frame(x) : cannot xtfrm data frames
10: In xtfrm.data.frame(x) : cannot xtfrm data frames
>
> proc.time()
user system elapsed
125.28 1.75 127.00
|
mAPKL.Rcheck/tests_x64/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.
> BiocGenerics:::testPackage("mAPKL")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Assign 60% as train data and 40% as test data
Saving density graph for breast$trainData in C:/Users/biocbuild/bbs-3.13-bioc/meat/mAPKL.Rcheck/tests_x64
Saving density graph for breast$testData in C:/Users/biocbuild/bbs-3.13-bioc/meat/mAPKL.Rcheck/tests_x64
b=10 b=20 b=30 b=40 b=50 b=60 b=70 b=80 b=90 b=100
b=110 b=120 b=130 b=140 b=150 b=160 b=170 b=180 b=190 b=200
b=210 b=220 b=230 b=240 b=250 b=260 b=270 b=280 b=290 b=300
b=310 b=320 b=330 b=340 b=350 b=360 b=370 b=380 b=390 b=400
b=410 b=420 b=430 b=440 b=450 b=460 b=470 b=480 b=490 b=500
b=510 b=520 b=530 b=540 b=550 b=560 b=570 b=580 b=590 b=600
b=610 b=620 b=630 b=640 b=650 b=660 b=670 b=680 b=690 b=700
b=710 b=720 b=730 b=740 b=750 b=760 b=770 b=780 b=790 b=800
b=810 b=820 b=830 b=840 b=850 b=860 b=870 b=880 b=890 b=900
b=910 b=920 b=930 b=940 b=950 b=960 b=970 b=980 b=990 b=1000
Please wait! The (KL) cluster indexing may take several minutes...
Asking for 22 number of clusters
fc according to limma
Loading required package: hgu133plus2.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: org.Hs.eg.db
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Negative samples: 8
Positive samples: 4
TN=6
FP=2
TP=3
FN=1
AUC=0.75
Accuracy=75.00
MCC=0.48
Specificity=0.75
Sensitivity=0.75
Assign 60% as train data and 40% as test data
RUNIT TEST PROTOCOL -- Fri Oct 15 01:39:32 2021
***********************************************
Number of test functions: 3
Number of errors: 0
Number of failures: 0
1 Test Suite :
mAPKL RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3
Number of errors: 0
Number of failures: 0
Warning messages:
1: In xtfrm.data.frame(x) : cannot xtfrm data frames
2: In xtfrm.data.frame(x) : cannot xtfrm data frames
3: In xtfrm.data.frame(x) : cannot xtfrm data frames
4: In .local(s, x = x, ...) : algorithm did not converge; turn on details
and call plot() to monitor net similarity. Consider
increasing 'maxits' and 'convits', and, if oscillations occur
also increasing damping factor 'lam'.
5: In .local(s, x = x, ...) : algorithm did not converge; turn on details
and call plot() to monitor net similarity. Consider
increasing 'maxits' and 'convits', and, if oscillations occur
also increasing damping factor 'lam'.
6: In .local(s, x = x, ...) : algorithm did not converge; turn on details
and call plot() to monitor net similarity. Consider
increasing 'maxits' and 'convits', and, if oscillations occur
also increasing damping factor 'lam'.
7: In .local(s, x = x, ...) : algorithm did not converge; turn on details
and call plot() to monitor net similarity. Consider
increasing 'maxits' and 'convits', and, if oscillations occur
also increasing damping factor 'lam'.
8: In xtfrm.data.frame(x) : cannot xtfrm data frames
9: In xtfrm.data.frame(x) : cannot xtfrm data frames
10: In xtfrm.data.frame(x) : cannot xtfrm data frames
>
> proc.time()
user system elapsed
121.62 0.90 122.53
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mAPKL.Rcheck/examples_i386/mAPKL-Ex.timings
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mAPKL.Rcheck/examples_x64/mAPKL-Ex.timings
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