Oliver M. Crook
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/bandle |
| git_branch: RELEASE_3_16 |
| git_last_commit: 8ab251f |
| git_last_commit_date: 2023-01-19 11:14:11 -0400 (Thu, 19 Jan 2023) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:59 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 bandle package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bandle.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 112/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bandle 1.2.2 (landing page) Oliver M. Crook
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: bandle |
| Version: 1.2.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bandle.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bandle_1.2.2.tar.gz |
| StartedAt: 2023-04-10 18:53:00 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 19:00:59 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 478.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: bandle.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bandle.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bandle_1.2.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/bandle.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bandle/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bandle’ version ‘1.2.2’
* package encoding: UTF-8
* 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 ‘bandle’ 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 ... NOTE
'library' or 'require' call to ‘Biobase’ which was already attached by Depends.
Please remove these calls from your code.
':::' call which should be '::': ‘dplyr:::summarise’
See the note in ?`:::` about the use of this operator.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
bandle-differentiallocalisation 21.343 0.575 21.977
bandle-gpfit 15.177 0.237 15.556
bandle 9.171 0.161 9.348
bandle-EFDR 8.139 0.299 8.462
bandle-predict 7.287 0.069 7.372
bandle-plots-translocations 7.204 0.099 7.316
bandle-process 6.697 0.102 6.843
bandle-plots-translocations-table 6.188 0.087 6.319
bandle-plots-convergence 6.157 0.094 6.265
bandle-prior 5.663 0.366 6.049
bandle-plots-prob 5.339 0.076 5.438
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘spelling.R’
Running ‘testthat.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-3.16-bioc/meat/bandle.Rcheck/00check.log’
for details.
bandle.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL bandle ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘bandle’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c Bessel2ndKind.cpp -o Bessel2ndKind.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c dmvtCpp.cpp -o dmvtCpp.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c leapfrogGPcpp.cpp -o leapfrogGPcpp.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c pg_sample.cpp -o pg_sample.o clang++ -mmacosx-version-min=10.13 -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 bandle.so Bessel2ndKind.o RcppExports.o dmvtCpp.o leapfrogGPcpp.o pg_sample.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -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 ld: warning: dylib (/usr/local/gfortran/lib/libgfortran.dylib) was built for newer macOS version (10.14) than being linked (10.13) ld: warning: dylib (/usr/local/gfortran/lib/libquadmath.dylib) was built for newer macOS version (10.14) than being linked (10.13) installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-bandle/00new/bandle/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function from function ‘posteriorEstimates’ in package ‘bandle’ Creating a generic function from function ‘bandleJoint’ in package ‘bandle’ ** 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 (bandle)
bandle.Rcheck/tests/spelling.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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.
> #if(requireNamespace('spelling', quietly = TRUE))
> # spelling::spell_check_test(vignettes = TRUE, error = FALSE,
> # skip_on_cran = TRUE)
>
> proc.time()
user system elapsed
0.195 0.067 0.254
bandle.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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.
> # The setting of R_TESTS exists to work around an R bug. See
> # https://github.com/hadley/testthat/issues/144
> # We should remove it when the issue is resolved.
> Sys.setenv("R_TESTS" = "")
>
> library("testthat")
> library("bandle")
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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, aperm, 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
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
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: MSnbase
Loading required package: mzR
Loading required package: Rcpp
Loading required package: ProtGenerics
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
This is MSnbase version 2.24.2
Visit https://lgatto.github.io/MSnbase/ to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:base':
trimws
Loading required package: pRoloc
Loading required package: MLInterfaces
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: IRanges
Loading required package: XML
Attaching package: 'annotate'
The following object is masked from 'package:mzR':
nChrom
Loading required package: cluster
Loading required package: BiocParallel
This is pRoloc version 1.38.2
Visit https://lgatto.github.io/pRoloc/ to get started.
Attaching package: 'bandle'
The following object is masked from 'package:pRoloc':
spatial2D
> library("pRolocdata")
This is pRolocdata version 1.36.0.
Use 'pRolocdata()' to list available data sets.
>
> test_check("bandle")
[1] "markers"
[1] "markers"
[1] "markers"
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%[1] "markers"
[1] "markers"
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%[1] "xx"
[1] "xx"
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%[1] "xx"
[1] "xx"
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%[1] "markers"
[1] "markers"
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%[1] "markers"
[1] "markers"
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%[1] "xx"
[1] "xx"
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%[1] "xx"
[1] "xx"
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%[1] "markers"
[1] "markers"
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%[1] "markers"
[1] "markers"
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%[1] "xx"
[1] "xx"
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%[1] "xx"
[1] "xx"
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%[1] "markers"
[1] "markers"
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%[1] "markers"
[1] "markers"
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%[1] "xx"
[1] "xx"
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%[1] "xx"
[1] "xx"
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%[1] "markers"
[1] "markers"
|
| | 0%
|
|==== | 5%
|
|======= | 10%
|
|========== | 15%
|
|============== | 20%
|
|================== | 25%
|
|===================== | 30%
|
|======================== | 35%
|
|============================ | 40%
|
|================================ | 45%
|
|=================================== | 50%
|
|====================================== | 55%
|
|========================================== | 60%
|
|============================================== | 65%
|
|================================================= | 70%
|
|==================================================== | 75%
|
|======================================================== | 80%
|
|============================================================ | 85%
|
|=============================================================== | 90%[1] "markers"
[1] "markers"
|
| | 0%
|
|==== | 5%
|
|======= | 10%
|
|========== | 15%
|
|============== | 20%
|
|================== | 25%
|
|===================== | 30%
|
|======================== | 35%
|
|============================ | 40%
|
|================================ | 45%
|
|=================================== | 50%
|
|====================================== | 55%
|
|========================================== | 60%
|
|============================================== | 65%
|
|================================================= | 70%
|
|==================================================== | 75%
|
|======================================================== | 80%
|
|============================================================ | 85%
|
|=============================================================== | 90%[1] "xx"
[1] "xx"
|
| | 0%
|
|==== | 5%
|
|======= | 10%
|
|========== | 15%
|
|============== | 20%
|
|================== | 25%
|
|===================== | 30%
|
|======================== | 35%
|
|============================ | 40%
|
|================================ | 45%
|
|=================================== | 50%
|
|====================================== | 55%
|
|========================================== | 60%
|
|============================================== | 65%
|
|================================================= | 70%
|
|==================================================== | 75%
|
|======================================================== | 80%
|
|============================================================ | 85%
|
|=============================================================== | 90%[1] "xx"
[1] "xx"
|
| | 0%
|
|==== | 5%
|
|======= | 10%
|
|========== | 15%
|
|============== | 20%
|
|================== | 25%
|
|===================== | 30%
|
|======================== | 35%
|
|============================ | 40%
|
|================================ | 45%
|
|=================================== | 50%
|
|====================================== | 55%
|
|========================================== | 60%
|
|============================================== | 65%
|
|================================================= | 70%
|
|==================================================== | 75%
|
|======================================================== | 80%
|
|============================================================ | 85%
|
|=============================================================== | 90%[1] "markers"
[1] "markers"
[1] "markers"
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%[1] "markers"
[1] "markers"
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%[1] "markers"
[1] "markers"
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%[1] "markers"
[1] "markers"
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%[1] "markers"
[1] "markers"
[1] "markers"
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%[1] "markers"
[1] "markers"
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%[1] "markers"
[1] "markers"
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%[1] "markers"
[1] "markers"
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%[1] "markers"
[1] "markers"
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%[1] "markers"
[1] "markers"
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%[1] "markers"
[1] "markers"
[1] "markers"
[1] "markers"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 36 ]
>
> proc.time()
user system elapsed
109.207 4.755 114.394
bandle.Rcheck/bandle-Ex.timings
| name | user | system | elapsed | |
| bandle-EFDR | 8.139 | 0.299 | 8.462 | |
| bandle-cpp | 0 | 0 | 0 | |
| bandle-differentiallocalisation | 21.343 | 0.575 | 21.977 | |
| bandle-gp | 0 | 0 | 0 | |
| bandle-gpfit | 15.177 | 0.237 | 15.556 | |
| bandle-internal | 0.385 | 0.010 | 0.395 | |
| bandle-meanOrganelle | 0.030 | 0.003 | 0.034 | |
| bandle-plots-convergence | 6.157 | 0.094 | 6.265 | |
| bandle-plots-prob | 5.339 | 0.076 | 5.438 | |
| bandle-plots-spatial | 0.000 | 0.000 | 0.005 | |
| bandle-plots-translocations-table | 6.188 | 0.087 | 6.319 | |
| bandle-plots-translocations | 7.204 | 0.099 | 7.316 | |
| bandle-predict | 7.287 | 0.069 | 7.372 | |
| bandle-prior | 5.663 | 0.366 | 6.049 | |
| bandle-process | 6.697 | 0.102 | 6.843 | |
| bandle-sim | 0.435 | 0.006 | 0.442 | |
| bandle | 9.171 | 0.161 | 9.348 | |
| method-mr | 1.795 | 0.025 | 1.828 | |