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I cannot require arrayQualityMetrics although I've downloaded it. What should I do?
library("arrayQualityMetrics")
# Error: package or namespace load failed for ‘arrayQualityMetrics’:
#.onLoad failed in loadNamespace() for 'httr', details:
# call: options()
#error: Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'NULL'
sessionInfo( )
#R version 4.1.1 (2021-08-10)
#Platform: x86_64-w64-mingw32/x64 (64-bit)
#Running under: Windows 10 x64 (build 19042)
#Matrix products: default
#locale:
#[1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 LC_MONETARY=Spanish_Spain.1252
#[4] LC_NUMERIC=C LC_TIME=C
#attached base packages:
#[1] stats4 parallel stats graphics grDevices utils datasets methods base
#other attached packages:
#[1] pd.mogene.2.1.st_3.14.1 DBI_1.1.1 RSQLite_2.2.8 oligo_1.56.0
#[5] Biostrings_2.60.2 GenomeInfoDb_1.28.4 XVector_0.32.0 IRanges_2.26.0
#[9] S4Vectors_0.30.2 Biobase_2.52.0 oligoClasses_1.54.0 BiocGenerics_0.38.0
#[13] knitr_1.36 readxl_1.3.1
#loaded via a namespace (and not attached):
#[1] MatrixGenerics_1.4.3 bit64_4.0.5 splines_4.1.1 foreach_1.5.1
#[5] BiocManager_1.30.16 affy_1.70.0 highr_0.9 blob_1.2.2
#[9] GenomeInfoDbData_1.2.6 cellranger_1.1.0 yaml_2.2.1 gcrma_2.64.0
#[13] pillar_1.6.4 lattice_0.20-44 digest_0.6.28 GenomicRanges_1.44.0
#[17] htmltools_0.5.2 preprocessCore_1.54.0 Matrix_1.3-4 pkgconfig_2.0.3
#[21] affxparser_1.64.1 zlibbioc_1.38.0 xtable_1.8-4 svglite_2.0.0
#[25] affyio_1.62.0 ff_4.0.4 tibble_3.1.5 ellipsis_0.3.2
#[29] cachem_1.0.6 SummarizedExperiment_1.22.0 cli_3.0.1 magrittr_2.0.1
#[33] crayon_1.4.1 memoise_2.0.0 evaluate_0.14 fansi_0.5.0
#[37] tools_4.1.1 lifecycle_1.0.1 matrixStats_0.61.0 affyPLM_1.68.0
#[41] DelayedArray_0.18.0 compiler_4.1.1 systemfonts_1.0.3 rlang_0.4.11
#[45] grid_4.1.1 RCurl_1.98-1.5 iterators_1.0.13 bitops_1.0-7
#[49] rmarkdown_2.11 codetools_0.2-18 R6_2.5.1 fastmap_1.1.0
#[53] bit_4.0.4 utf8_1.2.2 Rcpp_1.0.7 vctrs_0.3.8
#[57] xfun_0.26
When installing it I get
BiocManager::install("arrayQualityMetrics")
#'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
#replacement repositories:
# CRAN: https://cran.rstudio.com/
#Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10)
#Installation paths not writeable, unable to update packages
# path: C:/Program Files/R/R-4.1.1/library
# packages:
# lattice, mgcv, nlme, survival
#Old packages: 'rlang', 'xfun'
#Update all/some/none? [a/s/n]:
a
# There are binary versions available but the source versions are later:
# binary source needs_compilation
#rlang 0.4.11 0.4.12 TRUE
#xfun 0.26 0.27 TRUE
#trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/rlang_0.4.11.zip'
#Content type 'application/zip' length 1201275 bytes (1.1 MB)
#downloaded 1.1 MB
#trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/xfun_0.26.zip'
#Content type 'application/zip' length 358998 bytes (350 KB)
#downloaded 350 KB
#package ‘rlang’ successfully unpacked and MD5 sums checked
#Warning: cannot remove prior installation of package ‘rlang’
#Warning: restored ‘rlang’
#package ‘xfun’ successfully unpacked and MD5 sums checked
#Warning: cannot remove prior installation of package ‘xfun’
#Warning: restored ‘xfun’
#The downloaded binary packages are in
# C:\Users\Usuario\AppData\Local\Temp\RtmpM50TZw\downloaded_packages
#Warning messages:
#1: package(s) not installed when version(s) same as current; use `force = TRUE` to re-install: 'arrayQualityMetrics'
#2: In file.copy(savedcopy, lib, recursive = TRUE) :
# problem copying C:\Users\Usuario\Documents\R\win-library\4.1\00LOCK\rlang\libs\x64\rlang.dll to C:\Users\Usuario\Documents\R\win-#library\4.1\rlang\libs\x64\rlang.dll: Permission denied
#3: In file.copy(savedcopy, lib, recursive = TRUE) :
# problem copying C:\Users\Usuario\Documents\R\win-library\4.1\00LOCK\xfun\libs\x64\xfun.dll to C:\Users\Usuario\Documents\R\win-#library\4.1\xfun\libs\x64\xfun.dll: Permission denied
Great, glad you got it sorted.