Manuel Goepferich
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/LINC |
| Branch: RELEASE_3_10 |
| Last Commit: 5c7701c |
| Last Changed Date: 2019-10-29 13:10:05 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:44:12 -0400 (Wed, 15 Apr 2020).
| Package 905/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| LINC 1.14.0 Manuel Goepferich
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: LINC |
| Version: 1.14.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:LINC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings LINC_1.14.0.tar.gz |
| StartedAt: 2020-04-15 03:24:41 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:32:59 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 497.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: LINC.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:LINC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings LINC_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/LINC.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LINC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LINC’ version ‘1.14.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘LINC’ 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
* 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
justlinc,matrix: no visible global function definition for ‘plot’
Undefined global functions or variables:
plot
Consider adding
importFrom("graphics", "plot")
to your NAMESPACE file.
* 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 R/sysdata.rda ... NOTE
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
sysdata.rda 449Kb 299Kb xz
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
singlelinc-methods 78.105 6.243 85.260
getbio-methods 68.621 6.290 76.073
clusterlinc-methods 23.826 0.461 24.457
linc-methods 5.904 0.434 6.419
plotlinc-methods 5.720 0.230 5.990
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.10-bioc/meat/LINC.Rcheck/00check.log’
for details.
LINC.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL LINC
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘LINC’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Cppspear.cpp -o Cppspear.o
Cppspear.cpp:78:14: warning: unused variable 'qspear' [-Wunused-variable]
double qspear;double nfraction;
^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c LINC_init.c -o LINC_init.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c docdd.cpp -o docdd.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c doesd.cpp -o doesd.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o LINC.so Cppspear.o LINC_init.o RcppExports.o docdd.o doesd.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-LINC/00new/LINC/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘history’ in package ‘LINC’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (LINC)
LINC.Rcheck/tests/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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("LINC")
This is LINC - Co-Expression Analysis of lincRNAs
(Manuel Goepferich & Carl Herrmann)
Attaching package: 'LINC'
The following object is masked from 'package:utils':
history
removed 4 zero variance genes from input
removed genes with duplicated names
linc: gene system(s) assumed:
ENTREZID
linc: Correlation function with 'everything' called
linc: Computation of correlation matrix started
clusterlinc: computation for the correlation test started
clusterlinc: distance matrix called with the method dicedist
clusterlinc: co-expressed genes selected based on 'pvalCutOff'
removed 4 zero variance genes from input
removed genes with duplicated names
linc: gene system(s) assumed:
ENTREZID
linc: Correlation function with 'everything' called
linc: Computation of correlation matrix started
singlelinc: no test conducted, genes selected based on correlation values
singlelinc: co-expression analysis yielded 9 genes
singlelinc: The function enrichGO will be called.
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
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, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
removed 4 zero variance genes from input
removed genes with duplicated names
linc: gene system(s) assumed:
ENTREZID
linc: Correlation function with 'everything' called
linc: Computation of correlation matrix started
removed 4 zero variance genes from input
removed genes with duplicated names
linc: gene system(s) assumed:
ENTREZID
linc: Correlation function with 'everything' called
linc: Computation of correlation matrix started
clusterlinc: computation for the correlation test started
clusterlinc: distance matrix called with the method dicedist
clusterlinc: co-expressed genes selected based on 'pvalCutOff'
RUNIT TEST PROTOCOL -- Wed Apr 15 03:32:48 2020
***********************************************
Number of test functions: 4
Number of errors: 0
Number of failures: 0
1 Test Suite :
LINC RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4
Number of errors: 0
Number of failures: 0
Warning messages:
1: In linc(cor_test_mat, codingGenes = c(TRUE, FALSE, TRUE, TRUE, FALSE, :
Input 'object' contains infinite values
2: In linc(cor_test_mat, codingGenes = c(TRUE, FALSE, TRUE, TRUE, FALSE, :
Input 'object' contains infinite values
3: In singlelinc(linc_matrix, query = "17", onlycor = T, underth = F, :
'testFun' was supplied and 'onlycor' equals 'TRUE', here 'onlycor' has the higher priority
4: In linc(cor_test_mat, codingGenes = c(TRUE, FALSE, TRUE, TRUE, FALSE, :
Input 'object' contains infinite values
5: In linc(cor_test_mat, codingGenes = c(TRUE, FALSE, TRUE, TRUE, FALSE, :
Input 'object' contains infinite values
>
> proc.time()
user system elapsed
72.970 5.196 79.285
LINC.Rcheck/LINC-Ex.timings
| name | user | system | elapsed | |
| Arith-methods | 3.430 | 0.144 | 3.610 | |
| BRAIN_EXPR | 0.226 | 0.019 | 0.249 | |
| LINCbio-class | 0.001 | 0.000 | 0.001 | |
| LINCcluster-class | 0.000 | 0.000 | 0.001 | |
| LINCfeature-class | 0 | 0 | 0 | |
| LINCmatrix-class | 0.000 | 0.000 | 0.001 | |
| LINCsingle-class | 0.001 | 0.000 | 0.000 | |
| assignment-methods | 0.192 | 0.017 | 0.209 | |
| changeOrgDb | 0.182 | 0.017 | 0.200 | |
| clusterlinc-methods | 23.826 | 0.461 | 24.457 | |
| correlation-methods | 0.328 | 0.106 | 0.435 | |
| express-methods | 0.452 | 0.210 | 0.663 | |
| feature | 2.695 | 0.093 | 2.810 | |
| getbio-methods | 68.621 | 6.290 | 76.073 | |
| getcoexpr | 0.502 | 0.038 | 0.546 | |
| getlinc-methods | 0.263 | 0.022 | 0.287 | |
| history-methods | 0.225 | 0.023 | 0.251 | |
| justlinc-methods | 0.001 | 0.000 | 0.002 | |
| linCenvir-methods | 0.216 | 0.020 | 0.239 | |
| linc-methods | 5.904 | 0.434 | 6.419 | |
| linctable-methods | 0 | 0 | 0 | |
| plotlinc-methods | 5.72 | 0.23 | 5.99 | |
| querycluster | 0.483 | 0.023 | 0.509 | |
| results-methods | 0.224 | 0.017 | 0.242 | |
| singlelinc-methods | 78.105 | 6.243 | 85.260 | |