Hiroaki Kato
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/nuCpos |
| Branch: RELEASE_3_8 |
| Last Commit: 3451088 |
| Last Changed Date: 2019-01-04 13:06:15 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 12:11:56 -0400 (Tue, 16 Apr 2019).
| Package 1068/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| nuCpos 1.0.1 Hiroaki Kato
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: nuCpos |
| Version: 1.0.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:nuCpos.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings nuCpos_1.0.1.tar.gz |
| StartedAt: 2019-04-16 01:37:42 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:38:16 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 34.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: nuCpos.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:nuCpos.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings nuCpos_1.0.1.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/nuCpos.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nuCpos/DESCRIPTION’ ... OK
* this is package ‘nuCpos’ version ‘1.0.1’
* 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 ‘nuCpos’ 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 ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... 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 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 820Kb 495Kb bzip2
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
File ‘nuCpos/libs/nuCpos.so’:
Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
Objects: ‘nuCpos_1.o’, ‘nuCpos_2.o’
Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
Objects: ‘nuCpos_1.o’, ‘nuCpos_2.o’
Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
Objects: ‘nuCpos_1.o’, ‘nuCpos_2.o’
Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
(Fortran)
Objects: ‘nuCpos_1.o’, ‘nuCpos_2.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test_HBA.R’
Running ‘test_localHBA.R’
Running ‘test_mutNuCpos.R’
Running ‘test_predNuCposActLikePredNuPoP.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-3.8-bioc/meat/nuCpos.Rcheck/00check.log’
for details.
nuCpos.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL nuCpos ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘nuCpos’ ... ** libs gfortran -fPIC -Wall -g -O2 -c HBA_3.f90 -o HBA_3.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_nuCpos.c -o R_init_nuCpos.o gfortran -fPIC -Wall -g -O2 -c localHBA_3.f90 -o localHBA_3.o gfortran -fPIC -Wall -g -O2 -c nuCpos2_1.f90 -o nuCpos2_1.o gfortran -fPIC -Wall -g -O2 -c nuCpos2_2.f90 -o nuCpos2_2.o gfortran -fPIC -Wall -g -O2 -c nuCpos_1.f90 -o nuCpos_1.o gfortran -fPIC -Wall -g -O2 -c nuCpos_2.f90 -o nuCpos_2.o gfortran -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 nuCpos.so HBA_3.o R_init_nuCpos.o localHBA_3.o nuCpos2_1.o nuCpos2_2.o nuCpos_1.o nuCpos_2.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/nuCpos/libs ** R ** 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 * DONE (nuCpos)
nuCpos.Rcheck/tests/test_HBA.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> test_HBA <- function(){
+ load(system.file("extdata","inseq.RData",package="nuCpos"))
+ load(system.file("extdata","INSEQ_DNAString.RData",package="nuCpos"))
+ inseq.N <- gsub(pattern = "A", replacement = "N", inseq)
+ mm.HBA <- -5.108546
+ sc.HBA <- -2.460025
+ sp.HBA <- -2.627370
+ expect_equal(unname(HBA(inseq, species = "mm", silent = TRUE)),
+ mm.HBA, tolerance = 1.0e-6)
+ expect_equal(unname(HBA(inseq, species = "sc", silent = TRUE)),
+ sc.HBA, tolerance = 1.0e-6)
+ expect_equal(unname(HBA(inseq, species = "sp", silent = TRUE)),
+ sp.HBA, tolerance = 1.0e-6)
+ expect_equal(unname(HBA(INSEQ, species = "mm", silent = TRUE)),
+ mm.HBA, tolerance = 1.0e-6)
+ expect_equal(unname(HBA(INSEQ, species = "sc", silent = TRUE)),
+ sc.HBA, tolerance = 1.0e-6)
+ expect_equal(unname(HBA(INSEQ, species = "sp", silent = TRUE)),
+ sp.HBA, tolerance = 1.0e-6)
+ expect_true(is.na(HBA("AAA", species = "mm", silent = TRUE)))
+ expect_true(is.na(HBA(123, species = "mm", silent = TRUE)))
+ expect_true(is.na(HBA(inseq.N, species = "mm", silent = TRUE)))
+ }
>
> proc.time()
user system elapsed
0.257 0.060 0.295
nuCpos.Rcheck/tests/test_localHBA.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> test_localHBA <- function(){
+ load(system.file("extdata","inseq.RData",package="nuCpos"))
+ load(system.file("extdata","INSEQ_DNAString.RData",package="nuCpos"))
+ inseq.N <- gsub(pattern = "A", replacement = "N", inseq)
+ mm.lHBA <- c(-1.26144039, -1.60878614, 0.04168163,
+ 0.67028283, 0.64609413, -2.04965343, -2.87359702,
+ -0.23010702, -0.45807823, -0.46043330, -0.45175477,
+ 0.02487367, -0.30991794)
+ sc.lHBA <- c(-1.56140949, -1.62502354, 0.48885990,
+ 2.37615568, 2.90458625, -1.35195919, -3.13228907,
+ -0.32208031, 0.27650871, 0.01922002, 0.49787625,
+ -0.17151500, -1.27186158)
+ sp.lHBA <- c(-1.566757163, -2.249651890, 1.188983606,
+ 1.808008192, 2.304915648, -0.290338951, -1.741081053,
+ -0.093952092, 0.119058916, -1.335654721, -0.001721381,
+ 0.244317796, -0.968842314)
+ expect_equal(unname(localHBA(inseq, species = "mm", silent = TRUE)),
+ mm.lHBA, tolerance = 1.0e-6)
+ expect_equal(unname(localHBA(inseq, species = "sc", silent = TRUE)),
+ sc.lHBA, tolerance = 1.0e-6)
+ expect_equal(unname(localHBA(inseq, species = "sp", silent = TRUE)),
+ sp.lHBA, tolerance = 1.0e-6)
+ expect_equal(unname(localHBA(INSEQ, species = "mm", silent = TRUE)),
+ mm.lHBA, tolerance = 1.0e-6)
+ expect_equal(unname(localHBA(INSEQ, species = "sc", silent = TRUE)),
+ sc.lHBA, tolerance = 1.0e-6)
+ expect_equal(unname(localHBA(INSEQ, species = "sp", silent = TRUE)),
+ sp.lHBA, tolerance = 1.0e-6)
+ expect_true(is.na(localHBA("AAA", species = "mm", silent = TRUE)))
+ expect_true(is.na(localHBA(123, species = "mm", silent = TRUE)))
+ expect_true(is.na(localHBA(inseq.N, species = "mm", silent = TRUE)))
+ }
>
> proc.time()
user system elapsed
0.262 0.060 0.297
nuCpos.Rcheck/tests/test_mutNuCpos.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> test_mutNuCpos <- function(){
+ TALS <- paste(scan(file = system.file("extdata", "TALS.fasta",
+ package="nuCpos"), what = character(), skip = 1), sep = "",
+ collapse = "")
+ TTAGGGx12 <- paste(scan(file = system.file("extdata",
+ "TTAGGGx12.fasta", package="nuCpos"), what = character(),
+ skip = 1), sep = "", collapse = "")
+ results <- mutNuCpos(TALS, site = 1464, ins= TTAGGGx12, species="sc",
+ prob.dyad = TRUE, smoothHBA=TRUE, plot.window = 601,
+ ylim.HBA = c(-11, 0),
+ annotation = data.frame(name = "alpha2",
+ color = "purple", left = 1534, right = 1559), full = TRUE)
+ expect_equal(results$results$pstart[101], 0.0005225962, tolerance = 1.0e-8)
+ expect_equal(results$results$nucoccup[101], 0.9885672, tolerance = 1.0e-6)
+ expect_equal(results$results$viterbi[101], 1)
+ expect_equal(results$results$affinity[101], -0.89849, tolerance = 1.0e-5)
+ expect_equal(results$results$pos[101], -3673)
+ }
>
> proc.time()
user system elapsed
0.246 0.056 0.276
nuCpos.Rcheck/tests/test_predNuCposActLikePredNuPoP.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> test_predNuCposActLikePredNuPoP <- function(){
+ predNuCposActLikePredNuPoP(system.file("extdata", "test.seq",
+ package="nuCpos"), species="mm", smoothHBA=FALSE,
+ std=FALSE)
+ results <- read.table(file = "test.seq_Prediction4.txt", skip = 1)
+ expect_equal(results$V1[101], 101)
+ expect_equal(results$V2[101], 0.001)
+ expect_equal(results$V3[101], 0.742)
+ expect_equal(results$V4[101], 0)
+ expect_equal(results$V5[101], -2.303)
+ }
>
> proc.time()
user system elapsed
0.296 0.068 0.351
nuCpos.Rcheck/nuCpos-Ex.timings
| name | user | system | elapsed | |
| HBA | 0.013 | 0.005 | 0.020 | |
| localHBA | 0.005 | 0.002 | 0.009 | |
| mutNuCpos | 2.535 | 0.019 | 2.728 | |
| nuCpos-package | 0.090 | 0.009 | 0.101 | |
| predNuCpos | 0.219 | 0.008 | 0.231 | |