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perishky / meffil

Efficient algorithms for analyzing DNA methylation data.
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meffil.normalize.dataset() threw me an error #52

Open lovelymaoqin opened 1 year ago

lovelymaoqin commented 1 year ago

To whom it may concern, I was trying to use this function below, however, it threw me an error. Could you please give me some suggestions?

meffil.normalize.dataset(samplesheet, qc.file="qc/report.html", author="mao", study="IlluminaEpic", number.pcs=10)

Error in preprocessCore::normalize.quantiles.use.target(matrix(orig.signal), : ERROR; return code from pthread_create() is 22 Calls: meffil.normalize.dataset ... lapply -> FUN -> meffil.normalize.sample -> In addition: Warning messages: 1: In readChar(con, nchars = n) : truncating string with embedded nuls 2: In readChar(con, nchars = n) : truncating string with embedded nuls 3: The <scale> argument of guides() cannot be FALSE. Use "none" instead as of ggplot2 3.3.4. The deprecated feature was likely used in the meffil package. Please report the issue to the authors. 4: In readChar(con, nchars = n) : truncating string with embedded nuls 5: In readChar(con, nchars = n) : truncating string with embedded nuls Execution halted

Thank you,

MAO

perishky commented 1 year ago

Hi Mao,

With just the error message, I can only guess. It's possible that you have encountered this error:

https://support.bioconductor.org/p/122925/

If so, then reinstalling preprocessCore as follows should fix the problem:

BiocManager::install("preprocessCore", configure.args="--disable-threading", force = TRUE)

I could be more certain if I could see your sessionInfo() output.

Matt

lovelymaoqin commented 1 year ago

Hi Matt, Thanks for responding me. Actually, I reinstall the preprocessCore by
BiocManager::install("preprocessCore", configure.args="--disable-threading", force = TRUE)

However, it still threw me the same error. And the below is the sesseionInfo(). BTW, do we have the example dataset to test? Thanks, really appreciate it.

sessionInfo() R version 4.2.1 (2022-06-23) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux 8.7 (Ootpa)

Matrix products: default BLAS/LAPACK: /nas/longleaf/rhel8/apps/r/4.2.1/lib/libopenblas_haswellp-r0.3.20.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] meffil_1.3.5 preprocessCore_1.58.0 SmartSVA_0.1.3 RSpectra_0.16-1 isva_1.9
[6] JADE_2.0-3 qvalue_2.28.0 gdsfmt_1.32.0 statmod_1.5.0 quadprog_1.5-8
[11] DNAcopy_1.70.0 fastICA_1.2-3 multcomp_1.4-22 TH.data_1.1-1 survival_3.5-3
[16] mvtnorm_1.1-3 markdown_1.5 gridExtra_2.3 Cairo_1.6-0 knitr_1.42
[21] reshape2_1.4.4 plyr_1.8.8 sva_3.44.0 BiocParallel_1.30.4 genefilter_1.78.0
[26] mgcv_1.8-42 limma_3.52.4 sandwich_3.0-2 lmtest_0.9-40 zoo_1.8-11
[31] MASS_7.3-58.3 illuminaio_0.38.0 shiny_1.7.4 RPMM_1.25 cluster_2.1.4
[36] DT_0.27 IlluminaHumanMethylationEPICmanifest_0.3.0 Illumina450ProbeVariants.db_1.32.0 DMRcate_2.10.0 ChAMPdata_2.28.0
[41] minfi_1.42.0 bumphunter_1.38.0 locfit_1.5-9.7 iterators_1.0.14 foreach_1.5.2
[46] Biostrings_2.64.1 XVector_0.36.0 SummarizedExperiment_1.26.1 Biobase_2.56.0 MatrixGenerics_1.8.1
[51] matrixStats_0.63.0 GenomicRanges_1.48.0 GenomeInfoDb_1.32.4 IRanges_2.30.1 S4Vectors_0.34.0
[56] BiocGenerics_0.42.0 lmerTest_3.1-3 lme4_1.1-31 Matrix_1.5-3 lubridate_1.9.2
[61] forcats_1.0.0 stringr_1.5.0 dplyr_1.1.0 purrr_1.0.1 readr_2.1.4
[66] tidyr_1.3.0 ggplot2_3.4.1 tidyverse_2.0.0 feather_0.3.5 tibble_3.1.8
[71] data.table_1.14.8 CpGassoc_2.60 nlme_3.1-162

loaded via a namespace (and not attached): [1] rappdirs_0.3.3 rtracklayer_1.56.1 R.methodsS3_1.8.2 bit64_4.0.5
[5] DelayedArray_0.22.0 R.utils_2.12.2 rpart_4.1.19 KEGGREST_1.36.3
[9] RCurl_1.98-1.10 GEOquery_2.64.2 AnnotationFilter_1.20.0 generics_0.1.3
[13] GenomicFeatures_1.48.4 RSQLite_2.3.0 commonmark_1.8.1 bit_4.0.5
[17] tzdb_0.3.0 xml2_1.3.3 httpuv_1.6.9 IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0 [21] xfun_0.37 hms_1.1.2 evaluate_0.20 missMethyl_1.30.0
[25] promises_1.2.0.1 fansi_1.0.4 restfulr_0.0.15 scrime_1.3.5
[29] progress_1.2.2 readxl_1.4.2 dbplyr_2.3.1 DBI_1.1.3
[33] htmlwidgets_1.6.1 reshape_0.8.9 ellipsis_0.3.2 backports_1.4.1
[37] permute_0.9-7 annotate_1.74.0 biomaRt_2.52.0 deldir_1.0-6
[41] sparseMatrixStats_1.8.0 vctrs_0.5.2 ensembldb_2.20.2 cachem_1.0.7
[45] withr_2.5.0 Gviz_1.40.1 BSgenome_1.64.0 checkmate_2.1.0
[49] GenomicAlignments_1.32.1 prettyunits_1.1.1 mclust_6.0.0 ExperimentHub_2.4.0
[53] lazyeval_0.2.2 crayon_1.5.2 labeling_0.4.2 edgeR_3.38.4
[57] pkgconfig_2.0.3 ProtGenerics_1.28.0 nnet_7.3-18 rlang_1.0.6
[61] table1_1.4.3 lifecycle_1.0.3 filelock_1.0.2 BiocFileCache_2.4.0
[65] AnnotationHub_3.4.0 dichromat_2.0-0.1 cellranger_1.1.0 rngtools_1.5.2
[69] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1 base64_2.0.1 Rhdf5lib_1.18.2 boot_1.3-28.1
[73] base64enc_0.1-3 png_0.1-8 rjson_0.2.21 bitops_1.0-7
[77] R.oo_1.25.0 rhdf5filters_1.8.0 blob_1.2.3 DelayedMatrixStats_1.18.2
[81] doRNG_1.8.6 nor1mix_1.3-0 jpeg_0.1-10 scales_1.2.1
[85] memoise_2.0.1 magrittr_2.0.3 zlibbioc_1.42.0 compiler_4.2.1
[89] BiocIO_1.6.0 RColorBrewer_1.1-3 clue_0.3-64 Rsamtools_2.12.0
[93] cli_3.6.0 DSS_2.44.0 htmlTable_2.4.1 Formula_1.2-5
[97] tidyselect_1.2.0 stringi_1.7.12 highr_0.10 yaml_2.3.7
[101] askpass_1.1 latticeExtra_0.6-30 grid_4.2.1 VariantAnnotation_1.42.1
[105] tools_4.2.1 timechange_0.2.0 rstudioapi_0.14 foreign_0.8-84
[109] bsseq_1.32.0 farver_2.1.1 digest_0.6.31 BiocManager_1.30.20
[113] Rcpp_1.0.10 siggenes_1.70.0 writexl_1.4.2 BiocVersion_3.15.2
[117] later_1.3.0 org.Hs.eg.db_3.15.0 httr_1.4.5 AnnotationDbi_1.58.0
[121] biovizBase_1.44.0 colorspace_2.1-0 XML_3.99-0.13 splines_4.2.1
[125] multtest_2.52.0 xtable_1.8-4 nloptr_2.0.3 R6_2.5.1
[129] Hmisc_5.0-0 pillar_1.8.1 htmltools_0.5.4 mime_0.12
[133] glue_1.6.2 fastmap_1.1.1 minqa_1.2.5 interactiveDisplayBase_1.34.0
[137] beanplot_1.3.1 codetools_0.2-19 utf8_1.2.3 lattice_0.20-45
[141] numDeriv_2016.8-1.1 curl_5.0.0 gtools_3.9.4 openssl_2.0.5
[145] interp_1.1-3 rmarkdown_2.20 munsell_0.5.0 rhdf5_2.40.0

Hi Mao,

With just the error message, I can only guess. It's possible that you have encountered this error:

https://support.bioconductor.org/p/122925/

If so, then reinstalling preprocessCore as follows should fix the problem:

BiocManager::install("preprocessCore", configure.args="--disable-threading", force = TRUE)

I could be more certain if I could see your sessionInfo() output.

Matt

lovelymaoqin commented 1 year ago

Maybe this will help to find the issue.

BiocManager::install("preprocessCore", configure.args="--disable-threading", force=TRUE)

'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.15 (BiocManager 1.30.20), R 4.2.1 (2022-06-23) Installing package(s) 'preprocessCore' trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/preprocessCore_1.58.0.tar.gz' Content type 'application/x-tar' length 123998 bytes (121 KB) ================================================== downloaded 121 KB installing source* package ‘preprocessCore’ ... using staged installation 'config' variable 'CPP' is defunct checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for library containing pthread_create... -lpthread checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking if PTHREAD_STACK_MIN is defined... yes checking if R is using flexiblas... flexiblas not found. preprocessCore threading will not be disabled configure: Disabling threading for preprocessCore configure: creating ./config.status config.status: creating src/Makevars libs gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c R_colSummarize.c -o R_colSummarize.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c R_plmd_interfaces.c -o R_plmd_interfaces.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c R_plmr_interfaces.c -o R_plmr_interfaces.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c R_rlm_interfaces.c -o R_rlm_interfaces.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c R_subColSummarize.c -o R_subColSummarize.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c avg.c -o avg.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c avg_log.c -o avg_log.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c biweight.c -o biweight.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c init_package.c -o init_package.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c lm.c -o lm.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c log_avg.c -o log_avg.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c log_median.c -o log_median.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c matrix_functions.c -o matrix_functions.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c median.c -o median.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c median_log.c -o median_log.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c medianpolish.c -o medianpolish.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c plmd.c -o plmd.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c plmr.c -o plmr.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c psi_fns.c -o psi_fns.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c qnorm.c -o qnorm.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c rlm.c -o rlm.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c rlm_anova.c -o rlm_anova.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c rlm_se.c -o rlm_se.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c rma_background4.c -o rma_background4.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c rma_common.c -o rma_common.o gcc -I"/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -fpic -g -O2 -c weightedkerneldensity.c -o weightedkerneldensity.o gcc -shared -L/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/lib -L/usr/local/lib64 -o preprocessCore.so R_colSummarize.o R_plmd_interfaces.o R_plmr_interfaces.o R_rlm_interfaces.o R_subColSummarize.o R_subrcModel_interfaces.o avg.o avg_log.o biweight.o init_package.o lm.o log_avg.o log_median.o matrix_functions.o median.o median_log.o medianpolish.o plmd.o plmr.o psi_fns.o qnorm.o rlm.o rlm_anova.o rlm_se.o rma_background4.o rma_common.o weightedkerneldensity.o -lpthread -L/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/lib -lRlapack -L/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/lib -lRblas -lgfortran -lm -lquadmath -L/nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/lib -lR installing to /nas/longleaf/home/maoqin20/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-preprocessCore/00new/preprocessCore/libs R inst byte-compile and prepare package for lazy loading help installing help indices building package indices 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 (preprocessCore) The downloaded source packages are in '/work/appscr/r/maoqin20/RtmpK1GyLE/downloaded_packages' Installation paths not writeable, unable to update packages path: /nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/library packages: AICcmodavg, ape, aplot, arrow, berryFunctions, blob, bookdown, broom, cachem, car, checkmate, class, cli, coloc, commonmark, crul, dbplyr, deldir, dendextend, DEoptimR, distributional, dplyr, DT, dtplyr, evaluate, findpython, fitdistrplus, flexmix, flextable, FNN, fontawesome, fs, future.apply, gargle, gdata, gdistance, gdtools, gert, ggbeeswarm, ggplot2, ggsci, gimme, glmnet, googledrive, googlesheets4, graphlayouts, gtable, hexbin, Hmisc, hms, htmltools, htmlwidgets, httpuv, httr, httr2, igraph, interp, jsonlite, KernSmooth, knitr, later, lattice, lavaan, lme4, logistf, loo, lwgeom, magick, maptools, markdown, MASS, MatchIt, matchMulti, Matrix, matrixStats, mice, modelr, multcomp, mvtnorm, nnet, officer, OpenMx, openssl, parallelly, party, pillar, plotly, poppr, posterior, processx, profvis, ps, psych, qgraph, qpdf, qtl, quantmod, quantreg, rcartocolor, RcppArmadillo, RCurl, rgdal, rgeos, Rglpk, rjags, rlang, rmarkdown, Rmpi, robustbase, robustlmm, RSQLite, s2, sass, scattermore, scatterpie, scatterplot3d, segmented, seqinr, sf, Signac, sp, spatstat.data, spatstat.explore, spatstat.geom, spatstat.random, spatstat.sparse, spatstat.utils, spbabel, StanHeaders, statnet.common, strawr, survey, survival, sys, terra, testthat, TH.data, tibble, tigris, tinytex, TMB, truncnorm, tseries, tzdb, units, V8, vctrs, VGAM, viridis, viridisLite, vroom, waldo, wk, xfun, xgboost, XML, xml2, xts, zip, zoo

 

perishky commented 1 year ago

There does seem to be a problem in your installation (near the end): "Installation paths not writeable, unable to update packages path: /nas/longleaf/rhel8/apps/r/4.2.1/lib64/R/library packages" This suggests that the package could be installed but that you don't have the necessary file permissions. You could install R packages to your home directory where you do have file write permissions.

I encountered the same error as you in a later version of R (I was using 4.2.0 but have installed 4.3.0): Error in preprocessCore::normalize.quantiles.use.target(data, full.quantiles) : ERROR; return code from pthread_create() is 22 However, I was able to fix it by reinstalling preprocessCore with threading disabled: BiocManager::install("preprocessCore", configure.args="--disable-threading", force=T)