############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:ClustIRR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ClustIRR_1.5.31.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ClustIRR.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ClustIRR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ClustIRR’ version ‘1.5.31’ * 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 ‘ClustIRR’ can be installed ... WARNING Found the following significant warnings: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] See ‘/home/biocbuild/bbs-3.21-bioc/meat/ClustIRR.Rcheck/00install.out’ for details. * used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ * checking C++ specification ... OK * checking installed package size ... INFO installed size is 81.6Mb sub-directories of 1Mb or more: data 1.1Mb libs 79.4Mb * 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 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 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 ... NOTE get_community_ann: no visible binding for global variable ‘community’ Undefined global functions or variables: community * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'get_node_ann.Rd': get_node_ann Code: function(node_summary, ag_species, ag_genes) Docs: function(node_summary, ag_species, ag_gene) Argument names in code not in docs: ag_genes Argument names in docs not in code: ag_gene Mismatches in argument names: Position: 3 Code: ag_genes Docs: ag_gene * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'get_node_ann.Rd' ‘ag_gene’ Documented arguments not in \usage in Rd file 'get_node_ann.Rd': ‘ag_genes’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 shell scripts ... 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 ... INFO GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘ClustIRR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: detect_communities > ### Title: Graph-based community detection (GCD) > ### Aliases: detect_communities > > ### ** Examples > > # load package input data > data("CDR3ab", package = "ClustIRR") > a <- data.frame(CDR3a = CDR3ab[1:300, "CDR3a"], + CDR3b = CDR3ab[1:300, "CDR3b"], + clone_size = 1, + sample = "a") > > b <- data.frame(CDR3a = CDR3ab[201:400, "CDR3a"], + CDR3b = CDR3ab[201:400, "CDR3b"], + clone_size = 1, + sample = "b") > b$clone_size[1] <- 20 > > # run ClustIRR analysis > c <- c(cluster_irr(s = a), cluster_irr(s = b)) [1/2] annotating CDR3s... [2/2] clust_irr... Analyze database: 100.0% (300.0) Index database: 100.0% (300.0) Read queries: 100.0% (6103.0 Bytes) Read queries: 100.0% (6103.0 Bytes) Read queries: 100.0% (6103.0 Bytes) Read queries: 100.0% (6103.0 Bytes) Read queries: 100.0% (6103.0 Bytes) Search database: 100.0% (300.0) Write hits: 100.0% (842.0) Analyze database: 100.0% (300.0) Index database: 100.0% (300.0) Read queries: 100.0% (6052.0 Bytes) Read queries: 100.0% (6052.0 Bytes) Read queries: 100.0% (6052.0 Bytes) Read queries: 100.0% (6052.0 Bytes) Read queries: 100.0% (6052.0 Bytes) Search database: 100.0% (300.0) Write hits: 100.0% (647.0) [1/2] annotating CDR3s... [2/2] clust_irr... Analyze database: 100.0% (200.0) Index database: 100.0% (200.0) Read queries: 100.0% (4017.0 Bytes) Read queries: 100.0% (4017.0 Bytes) Read queries: 100.0% (4017.0 Bytes) Read queries: 100.0% (4017.0 Bytes) Search database: 100.0% ( Write hits: 100.0% (288.0) 200.0) Write hits: 100.0% (427.0) Analyze database: 100.0% (200.0) Index database: 100.0% (200.0) Read queries: 100.0% (3991.0 Bytes) Read queries: 100.0% (3991.0 Bytes) Read queries: 100.0% (3991.0 Bytes) Read queries: 100.0% (3991.0 Bytes) Search database: 100.0% (200.0) Write hits: 100.0% (349.0) > > # get joint graph > jg <- get_joint_graph(clust_irrs = c) [1/2] generating graphs... Error: MultisessionFuture (future_lapply-1) failed to call grmall() on cluster RichSOCKnode #1 (PID 1829689 on localhost ‘localhost’). The reason reported was ‘error reading from connection’. Post-mortem diagnostic: No process exists with this PID, i.e. the localhost worker is no longer alive. The total size of the 15 globals exported is 465.22 KiB. The three largest globals are ‘...future.elements_ii’ (361.43 KiB of class ‘list’), ‘...future.FUN’ (43.05 KiB of class ‘function’) and ‘graph_from_data_frame’ (19.77 KiB of class ‘function’) Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed dco 203.474 0.62 211.488 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 3 WARNINGs, 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/ClustIRR.Rcheck/00check.log’ for details.