* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/msig.Rcheck’ * using R Under development (unstable) (2024-03-16 r86144) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 13.2.1 20231011 (Red Hat 13.2.1-4) GNU Fortran (GCC) 13.2.1 20231011 (Red Hat 13.2.1-4) * running under: Fedora Linux 38 (Workstation Edition) * using session charset: UTF-8 * checking for file ‘msig/DESCRIPTION’ ... OK * this is package ‘msig’ version ‘1.0’ * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘msig’ can be installed ... OK * checking package 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 code 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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 line widths ... 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 ... OK * checking examples ... OK * checking examples with --run-donttest ... ERROR Running examples in ‘msig-Ex.R’ failed The error most likely occurred in: > ### Name: browse_msig > ### Title: Retrieve Gene set Names from MSigDB database Retrieve gene set > ### names from MSigDB database by the gene set name and collection. the > ### search filed is gene name. > ### Aliases: browse_msig > > ### ** Examples > > ## No test: > # missing genSetName and collection to get all gene set names > x <- browse_msig() gene sets: 0 > # search for gene names include immune > x <- browse_msig('immune') gene sets: 0 > > x |> + msig_view('cells','response','to','m') Warning in ensure_len_html(link, nrows, "link") : The number of provided values in link does not equal to the number of rows. Error in xml_children(x)[[search]] : subscript out of bounds Calls: msig_view -> -> column_spec_html -> xml_child Execution halted * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 1 ERROR See ‘/data/blackswan/ripley/R/packages/tests-devel/msig.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 1:00.48, 46.76 + 7.52