Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:08:27 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 |
To the developers/maintainers of the nuCpos package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/nuCpos.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1309/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
nuCpos 1.12.0 (landing page) Hiroaki Kato
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: nuCpos |
Version: 1.12.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nuCpos.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nuCpos_1.12.0.tar.gz |
StartedAt: 2022-04-12 16:13:36 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 16:14:15 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 39.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: nuCpos.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nuCpos.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nuCpos_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/nuCpos.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘nuCpos/DESCRIPTION’ ... OK * this is package ‘nuCpos’ version ‘1.12.0’ * 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 ‘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 ... 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 ... 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 824Kb 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.14-bioc/meat/nuCpos.Rcheck/00check.log’ for details.
nuCpos.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL nuCpos ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘nuCpos’ ... ** using staged installation ** libs gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c HBA_3.f90 -o HBA_3.o clang -mmacosx-version-min=10.13 -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 -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c localHBA_3.f90 -o localHBA_3.o gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c nuCpos2_1.f90 -o nuCpos2_1.o gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c nuCpos2_2.f90 -o nuCpos2_2.o gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c nuCpos_1.f90 -o nuCpos_1.o gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c nuCpos_2.f90 -o nuCpos_2.o clang -mmacosx-version-min=10.13 -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 -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-nuCpos/00new/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 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 (nuCpos)
nuCpos.Rcheck/tests/test_HBA.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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 0.282 0.071 0.326
nuCpos.Rcheck/tests/test_localHBA.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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 0.311 0.071 0.356
nuCpos.Rcheck/tests/test_mutNuCpos.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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], 0.0005697254, tolerance = 1.0e-8) + expect_equal(results$results$nucoccup[101], 0.9874718, 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 0.306 0.076 0.356
nuCpos.Rcheck/tests/test_predNuCposActLikePredNuPoP.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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 0.272 0.069 0.315
nuCpos.Rcheck/nuCpos-Ex.timings
name | user | system | elapsed | |
HBA | 0.017 | 0.003 | 0.019 | |
localHBA | 0.003 | 0.002 | 0.005 | |
mutNuCpos | 2.059 | 0.023 | 2.187 | |
nuCpos-package | 0.080 | 0.008 | 0.088 | |
predNuCpos | 0.226 | 0.014 | 0.241 | |