Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:00 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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 distinct package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/distinct.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 538/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
distinct 1.11.0 (landing page) Simone Tiberi
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: distinct |
Version: 1.11.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:distinct.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings distinct_1.11.0.tar.gz |
StartedAt: 2023-02-07 00:01:16 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 00:11:56 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 640.0 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: distinct.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:distinct.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings distinct_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/distinct.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘distinct/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘distinct’ version ‘1.11.0’ * 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 ‘distinct’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ * checking installed package size ... NOTE installed size is 8.3Mb sub-directories of 1Mb or more: data 1.0Mb libs 7.0Mb * 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 Namespace in Imports field not imported from: ‘Rfast’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE perm_test_parallel_R: no visible binding for global variable ‘cl_id’ perm_test_parallel_covariates_R: no visible binding for global variable ‘cl_id’ plot_cdfs: no visible binding for global variable ‘group’ plot_densities: no visible binding for global variable ‘group’ Undefined global functions or variables: cl_id group * 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 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 $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘distinct-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: distinct_test > ### Title: Test for differential state between two groups of samples, based > ### on scRNA-seq data. > ### Aliases: distinct_test > > ### ** Examples > > # load the input data: > data("Kang_subset", package = "distinct") > Kang_subset class: SingleCellExperiment dim: 100 9517 metadata(1): experiment_info assays(2): logcounts cpm rownames(100): ISG15 SYF2 ... MX2 PDXK rowData names(0): colnames: NULL colData names(3): stim cell sample_id reducedDimNames(0): mainExpName: NULL altExpNames(0): > > # create the design of the study: > samples = Kang_subset@metadata$experiment_info$sample_id > group = Kang_subset@metadata$experiment_info$stim > design = model.matrix(~group) > # rownames of the design must indicate sample ids: > rownames(design) = samples > design (Intercept) groupstim ctrl_107 1 0 ctrl_1015 1 0 ctrl_101 1 0 stim_101 1 1 stim_1015 1 1 stim_107 1 1 attr(,"assign") [1] 0 1 attr(,"contrasts") attr(,"contrasts")$group [1] "contr.treatment" > > # Note that the sample names in `colData(x)$name_sample` have to be the same ones as those in `rownames(design)`. > rownames(design) [1] "ctrl_107" "ctrl_1015" "ctrl_101" "stim_101" "stim_1015" "stim_107" > unique(SingleCellExperiment::colData(Kang_subset)$sample_id) [1] ctrl_107 ctrl_1015 ctrl_101 stim_101 stim_1015 stim_107 Levels: ctrl_101 ctrl_1015 ctrl_107 stim_101 stim_1015 stim_107 > > # In order to obtain a finer ranking for the most significant genes, if computational resources are available, we encourage users to increase P_4 (i.e., the number of permutations when a raw p-value is < 0.001) and set P_4 = 20,000 (by default P_4 = 10,000). > > # The group we would like to test for is in the second column of the design, therefore we will specify: column_to_test = 2 > > set.seed(61217) > res = distinct_test( + x = Kang_subset, + name_assays_expression = "logcounts", + name_cluster = "cell", + design = design, + column_to_test = 2, + min_non_zero_cells = 20, + n_cores = 2) 2 groups of samples provided Data loaded, starting differential testing Error in unserialize(socklist[[n]]) : error reading from connection Calls: distinct_test ... recvOneData -> recvOneData.SOCKcluster -> unserialize Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 2. └─distinct:::perm_test_parallel_R(...) 3. ├─... %dorng% ... 4. │ └─base::do.call(`%dopar%`, list(obj, ex), envir = parent.frame()) 5. └─foreach (local) `<fn>`(...) 6. └─e$fun(obj, substitute(ex), parent.frame(), e$data) 7. └─parallel::clusterApplyLB(cl, argsList, evalWrapper) 8. └─parallel:::dynamicClusterApply(cl, fun, length(x), argfun) 9. └─parallel:::recvOneResult(cl) 10. ├─parallel:::recvOneData(cl) 11. └─parallel:::recvOneData.SOCKcluster(cl) 12. └─base::unserialize(socklist[[n]]) [ FAIL 1 | WARN 1 | SKIP 0 | PASS 7 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘distinct.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 4 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/distinct.Rcheck/00check.log’ for details.
distinct.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL distinct ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘distinct’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include' -I/usr/local/include -fPIC -g -O2 -Wall -c Perm.cpp -o Perm.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include' -I/usr/local/include -fPIC -g -O2 -Wall -c Perm_covariates.cpp -o Perm_covariates.o In file included from /home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast.h:5, from Perm_covariates.cpp:2: /home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:553: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 553 | #pragma omp parallel for | /home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:604: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 604 | #pragma omp parallel for | /home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:621: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 621 | #pragma omp parallel for | /home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:639: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 639 | #pragma omp parallel for | /home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:654: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 654 | #pragma omp parallel for | /home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:669: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 669 | #pragma omp parallel for | Perm_covariates.cpp: In function ‘arma::vec my_rint_reg(const mat&, const vec&, Rcpp::IntegerVector, const unsigned int&, const unsigned int&, const double&, const unsigned int&)’: Perm_covariates.cpp:189:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 189 | for(int i=0;i<p;i++) | ~^~ Perm_covariates.cpp:210:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 210 | while(i++<maxiters && sum(abs(b2-b1.col(0))) > tol) { | ~~~^~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include' -I/usr/local/include -fPIC -g -O2 -Wall -c Perm_covariates_parallel.cpp -o Perm_covariates_parallel.o In file included from /home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast.h:5, from Perm_covariates_parallel.cpp:2: /home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:553: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 553 | #pragma omp parallel for | /home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:604: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 604 | #pragma omp parallel for | /home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:621: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 621 | #pragma omp parallel for | /home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:639: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 639 | #pragma omp parallel for | /home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:654: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 654 | #pragma omp parallel for | /home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:669: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 669 | #pragma omp parallel for | Perm_covariates_parallel.cpp: In function ‘arma::vec my_rint_reg_parallel(const mat&, const vec&, Rcpp::IntegerVector, const unsigned int&, const unsigned int&, const double&, const unsigned int&)’: Perm_covariates_parallel.cpp:189:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 189 | for(int i=0;i<p;i++) | ~^~ Perm_covariates_parallel.cpp:210:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 210 | while(i++<maxiters && sum(abs(b2-b1.col(0))) > tol) { | ~~~^~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include' -I/usr/local/include -fPIC -g -O2 -Wall -c Perm_parallel.cpp -o Perm_parallel.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o distinct.so Perm.o Perm_covariates.o Perm_covariates_parallel.o Perm_parallel.o RcppExports.o -llapack -L/home/biocbuild/bbs-3.17-bioc/R/lib -lRblas -lgfortran -lm -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-distinct/00new/distinct/libs ** R ** data ** 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 (distinct)
distinct.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (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. > library(testthat) > library(distinct) > test_check("distinct") [ FAIL 1 | WARN 1 | SKIP 0 | PASS 7 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_distinct_test.R:12'): distinct_test() works faultlessly. ─────── Error in `unserialize(socklist[[n]])`: error reading from connection Backtrace: ▆ 1. └─distinct::distinct_test(...) at test_distinct_test.R:12:2 2. └─distinct:::perm_test_parallel_R(...) 3. ├─... %dorng% ... 4. │ └─base::do.call(`%dopar%`, list(obj, ex), envir = parent.frame()) 5. └─foreach (local) `<fn>`(...) 6. └─e$fun(obj, substitute(ex), parent.frame(), e$data) 7. └─parallel::clusterApplyLB(cl, argsList, evalWrapper) 8. └─parallel:::dynamicClusterApply(cl, fun, length(x), argfun) 9. └─parallel:::recvOneResult(cl) 10. ├─parallel:::recvOneData(cl) 11. └─parallel:::recvOneData.SOCKcluster(cl) 12. └─base::unserialize(socklist[[n]]) [ FAIL 1 | WARN 1 | SKIP 0 | PASS 7 ] Error: Test failures Execution halted
distinct.Rcheck/distinct-Ex.timings
name | user | system | elapsed | |
Kang_subset | 0 | 0 | 0 | |