| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:41 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1353/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| nuCpos 1.17.0 (landing page) Hiroaki Kato
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: nuCpos |
| Version: 1.17.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:nuCpos.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings nuCpos_1.17.0.tar.gz |
| StartedAt: 2022-12-29 01:54:28 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 01:55:01 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 33.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: nuCpos.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:nuCpos.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings nuCpos_1.17.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/nuCpos.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'nuCpos/DESCRIPTION' ... OK
* this is package 'nuCpos' version '1.17.0'
* 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 'nuCpos' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* 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 824Kb 495Kb bzip2
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* 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_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
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/nuCpos.Rcheck/00check.log'
for details.
nuCpos.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL nuCpos ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'nuCpos' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 12.2.0' using Fortran compiler: 'GNU Fortran (GCC) 12.2.0' gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c HBA_3.f90 -o HBA_3.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_nuCpos.c -o R_init_nuCpos.o gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c localHBA_3.f90 -o localHBA_3.o gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c nuCpos2_1.f90 -o nuCpos2_1.o gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c nuCpos2_2.f90 -o nuCpos2_2.o gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c nuCpos_1.f90 -o nuCpos_1.o gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c nuCpos_2.f90 -o nuCpos_2.o gcc -shared -s -static-libgcc -o nuCpos.dll tmp.def HBA_3.o R_init_nuCpos.o localHBA_3.o nuCpos2_1.o nuCpos2_2.o nuCpos_1.o nuCpos_2.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -lgfortran -lm -lquadmath -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-nuCpos/00new/nuCpos/libs/x64 ** 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 ** 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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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.
> 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
0.20 0.04 0.20
nuCpos.Rcheck/tests/test_localHBA.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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.
> 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
0.10 0.07 0.15
nuCpos.Rcheck/tests/test_predNuCposActLikePredNuPoP.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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.
> 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
0.14 0.09 0.17
nuCpos.Rcheck/nuCpos-Ex.timings
| name | user | system | elapsed | |
| HBA | 0 | 0 | 0 | |
| localHBA | 0.02 | 0.00 | 0.01 | |
| nuCpos-package | 0.03 | 0.03 | 0.08 | |
| predNuCpos | 0.11 | 0.03 | 0.14 | |