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Dear All
I would like to install DESeq2 for DE analysis.
After I type the following script
if (!requireNamespace("BiocManager", quietly = TRUE))
+ install.packages("BiocManager") BiocManager::install("DESeq2")
The following comes out:
package ‘backports’ successfully unpacked and MD5 sums checked
package ‘bit64’ successfully unpacked and MD5 sums checked
package ‘callr’ successfully unpacked and MD5 sums checked
package ‘glue’ successfully unpacked and MD5 sums checked
package ‘Hmisc’ successfully unpacked and MD5 sums checked
package ‘jsonlite’ successfully unpacked and MD5 sums checked
package ‘MASS’ successfully unpacked and MD5 sums checked
package ‘mgcv’ successfully unpacked and MD5 sums checked
package ‘nlme’ successfully unpacked and MD5 sums checked
package ‘processx’ successfully unpacked and MD5 sums checked
package ‘ps’ successfully unpacked and MD5 sums checked
package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
package ‘stringi’ successfully unpacked and MD5 sums checked
package ‘vctrs’ successfully unpacked and MD5 sums checked
package ‘xfun’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages
installing the source package ‘htmlTable’
trying URL 'https://cran.rstudio.com/src/contrib/htmlTable_2.1.0.tar.gz'
Content type 'application/x-gzip' length 421796 bytes (411 KB)
downloaded 411 KB
* installing *source* package 'htmlTable' ...
** package 'htmlTable' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'htmlTable'
finding HTML links ... done
SCB html
addStyles html
concatHtmlTables html
getHtmlTableStyle html
getHtmlTableTheme html
hasHtmlTableStyle html
htmlTable html
htmlTableWidget-shiny html
htmlTableWidget html
innerJoinByCommonCols html
interactiveTable html
outputInt html
prAddCells html
prAddEmptySpacerCell html
prAddSemicolon2StrEnd html
prAttr4RgroupAdd html
prBindDataListIntoColumns html
prConvertDfFactors html
prEscapeHtml html
prExtractElementsAndConvertToTbl html
prGetAlign html
prGetCgroupHeader html
prGetRgroupLine html
prGetRowlabelPos html
prGetScriptString html
prGetStyle html
prGetThead html
prIsNotebook html
prMergeClr html
prPrepInputMatrixDimensions html
prPrepareAlign html
prPrepareCgroup html
prPrepareColors html
prPrepareCss html
prSkipRownames html
prTblNo html
prepGroupCounts html
pvalueFormatter html
setHtmlTableTheme html
splitLines4Table html
tblNoLast html
tblNoNext html
tidyHtmlTable html
txtInt html
txtMergeLines html
txtPval html
txtRound html
vector2string html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (htmlTable)
The downloaded source packages are in
‘C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages’
However, the function cannot be found when the following augment was typed:
DESeq.ds <- DESeqDataSetFromMatrix(countData=Fruit_ripening_TPM)
Error in DESeqDataSetFromMatrix(countData = Fruit_ripening_TPM) :
could not find function "DESeqDataSetFromMatrix"
Then, I tried to load the package but following comes out.
library("DESeq2")
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply,
parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval,
evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order,
paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which, which.max, which.min
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Attaching package: ‘IRanges’
The following object is masked from ‘package:grDevices’:
windows
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: ‘matrixStats’
The following objects are masked from ‘package:Biobase’:
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: ‘DelayedArray’
The following objects are masked from ‘package:matrixStats’:
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from ‘package:base’:
aperm, apply, rowsum
Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘XML’
In addition: Warning messages:
1: package ‘S4Vectors’ was built under R version 3.6.3
2: package ‘IRanges’ was built under R version 3.6.2
3: package ‘GenomeInfoDb’ was built under R version 3.6.3
4: package ‘SummarizedExperiment’ was built under R version 3.6.2
5: package ‘DelayedArray’ was built under R version 3.6.3
6: package ‘matrixStats’ was built under R version 3.6.3
7: package ‘BiocParallel’ was built under R version 3.6.2
FYI, my R version is 3.6.1. Someone from other post recommend me to install XML.
> install.packages("XML")
Installing package into ‘C:/Users/ASUS/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Warning: unable to access index for repository https://wbc.upm.edu.my/cran/src/contrib:
cannot open URL 'https://wbc.upm.edu.my/cran/src/contrib/PACKAGES'
Warning: unable to access index for repository https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6:
cannot open URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/PACKAGES'
Warning message:
package ‘XML’ is not available (for R version 3.6.1)
However, still not successful.
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)
Matrix products: default
locale:
[1] LC_COLLATE=English_Malaysia.1252 LC_CTYPE=English_Malaysia.1252 LC_MONETARY=English_Malaysia.1252
[4] LC_NUMERIC=C LC_TIME=English_Malaysia.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] SummarizedExperiment_1.16.1 DelayedArray_0.12.3 BiocParallel_1.20.1 matrixStats_0.56.0
[5] Biobase_2.46.0 GenomicRanges_1.38.0 GenomeInfoDb_1.22.1 IRanges_2.20.2
[9] S4Vectors_0.24.4 BiocGenerics_0.32.0
loaded via a namespace (and not attached):
[1] xfun_0.17 splines_3.6.1 lattice_0.20-41 colorspace_1.4-1 vctrs_0.3.4
[6] htmltools_0.5.0 base64enc_0.1-3 survival_3.2-3 rlang_0.4.7 pillar_1.4.6
[11] foreign_0.8-71 glue_1.4.2 RColorBrewer_1.1-2 jpeg_0.1-8.1 GenomeInfoDbData_1.2.2
[16] lifecycle_0.2.0 stringr_1.4.0 zlibbioc_1.32.0 munsell_0.5.0 gtable_0.3.0
[21] htmlwidgets_1.5.1 latticeExtra_0.6-29 knitr_1.29 htmlTable_2.1.0 Rcpp_1.0.5
[26] xtable_1.8-4 scales_1.1.1 backports_1.1.9 checkmate_2.0.0 BiocManager_1.30.10
[31] Hmisc_4.4-1 XVector_0.26.0 gridExtra_2.3 ggplot2_3.3.2 png_0.1-7
[36] digest_0.6.25 stringi_1.4.6 grid_3.6.1 tools_3.6.1 bitops_1.0-6
[41] magrittr_1.5 RCurl_1.98-1.2 tibble_3.0.3 Formula_1.2-3 cluster_2.1.0
[46] crayon_1.3.4 pkgconfig_2.0.3 ellipsis_0.3.1 Matrix_1.2-18 data.table_1.13.0
[51] rstudioapi_0.11 R6_2.4.1 rpart_4.1-15 nnet_7.3-14 compiler_3.6.1
May I know is there any other approach I can try?
I see
so I would try to use
BiocManager::install("XML"). But I guess you have many problems with your installation, and I'd suggestand then updating the packages that command indicates.
Dear Martin
Thanks for your suggestion. I have tried your suggestion and also updating the packages that command indicates. I even tried BiocManager::install("XML") but all failed as shown below. Any other suggestion? Should I update the Bioconductor to latest version instead?
R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18362)
Matrix products: default
locale: [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 [4] LCNUMERIC=C LCTIME=English_Malaysia.1252
attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0
[5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2
[9] S4Vectors0.24.4 BiocGenerics0.32.0
loaded via a namespace (and not attached): [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4
[6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6
[11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0
[21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5
[26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10
[31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7
[36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6
[41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0
[46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0
[51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1
Bioconductor version '3.10'
create a valid installation with
BiocManager::install(c( "htmlTable", "xfun" ), update = TRUE, ask = FALSE)
more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date
Warning message: 0 packages out-of-date; 2 packages too new
trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' Content type 'application/zip' length 233860 bytes (228 KB) downloaded 228 KB
package ‘htmlTable’ successfully unpacked and MD5 sums checked 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\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, spatial, survival Warning message: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\ASUS\Documents\R\win-library\3.6\00LOCK\xfun\libs\x64\xfun.dll to C:\Users\ASUS\Documents\R\win-library\3.6\xfun\libs\x64\xfun.dll: Permission denied
package ‘XML’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, spatial, survival
Hmm, but it says
package ‘XML’ successfully unpacked and MD5 sums checkedit looks mostly like these have been successful?Dear Martin
Sorry, I'm newbie. Just realize that I need to write the script "library("DESeq2")" before I proceed. It is working now.
Really thanks so much for your help.