############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:crossmeta.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings crossmeta_1.27.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/crossmeta.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * checking for file ‘crossmeta/DESCRIPTION’ ... OK * this is package ‘crossmeta’ version ‘1.27.0’ * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘crossmeta’ 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘RCurl’ ‘XML’ 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 ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed symbol_annot 21.422 2.475 28.357 diff_expr 22.330 1.272 24.047 es_meta 14.141 0.469 14.702 setup_prev 6.013 1.385 8.270 get_raw 0.595 0.065 9.218 * 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: ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-two-channel.R:60:3'): crossmeta produces similar results to limma ── Error in `limma::intraspotCorrelation(MA, mod)`: statmod package required but is not installed Backtrace: ▆ 1. └─crossmeta::diff_expr(...) at test-two-channel.R:60:2 2. └─crossmeta::run_limma(eset, annot, svobj, numsv) 3. └─crossmeta:::fit_lm(...) 4. └─crossmeta:::run_lmfit(eset, mod, rna_seq) 5. └─limma::intraspotCorrelation(MA, mod) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 19 ] 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 ... ‘crossmeta-vignette.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘crossmeta-vignette.Rmd’ using rmarkdown add_sources package:crossmeta R Documentation _A_d_d _s_a_m_p_l_e _s_o_u_r_c_e _i_n_f_o_r_m_a_t_i_o_n _f_o_r _m_e_t_a-_a_n_a_l_y_s_i_s. _D_e_s_c_r_i_p_t_i_o_n: User selects a tissue source for each contrast and indicates any sources that should be paired. This step is required if you would like to perform source-specific effect-size/pathway meta-analyses. _U_s_a_g_e: add_sources(diff_exprs, data_dir = getwd(), postfix = NULL) _A_r_g_u_m_e_n_t_s: diff_exprs: Previous result of 'diff_expr', which can be reloaded using 'load_diff'. data_dir: String specifying directory of GSE folders. postfix: Optional string to append to saved results. Useful if need to run multiple meta-analyses on the same series but with different contrasts. _D_e_t_a_i_l_s: The *Sources* tab is used to add a source for each contrast. To do so: click the relevant contrast rows, search for a source in the _Sample source_ dropdown box, and then click the _Add_ button. The *Pairs* tab is used to indicate sources that should be paired (treated as the same source for subsequent effect-size and pathway meta-analyses). To do so: select at least two sources from the _Paired sources_ dropdown box, and then click the _Add_ button. For each GSE, analysis results with added sources/pairs are saved in the corresponding GSE folder (in 'data_dir') that was created by 'get_raw'. _V_a_l_u_e: Same as 'diff_expr' with added slots for each GSE in 'diff_exprs': sources: Named vector specifying selected sample source for each contrast. Vector names identify the contrast. pairs: List of character vectors indicating tissue sources that should be treated as the same source for subsequent effect-size and pathway meta-analyses. _E_x_a_m_p_l_e_s: library(lydata) # load result of previous call to diff_expr: data_dir <- system.file("extdata", package = "lydata") gse_names <- c("GSE9601", "GSE34817") anals <- load_diff(gse_names, data_dir) # run shiny GUI to add tissue sources # anals <- add_sources(anals, data_dir) * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 NOTE See ‘/home/biocbuild/bbs-3.18-bioc/meat/crossmeta.Rcheck/00check.log’ for details.