Deseq2 installed, but there is no package called ‘Biostrings’
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Entering edit mode
@8cefaead
Last seen 2.2 years ago
United States

I got this message every time: 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 ‘Biostrings’ In addition: Warning message: package ‘DESeq2’ was built under R version 4.1.1

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.18 compiler_4.1.0      tools_4.1.0     

if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install(version = "3.14", force = TRUE, dependencies = TRUE)
BiocManager::install("DESeq2",force = TRUE, dependencies = TRUE)
BiocManager::install("Biostrings",force = TRUE, dependencies = TRUE)

#I may miss something because codes were copy and paste here#

Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.0 (2021-05-18)
Installing package(s) 'DESeq2'
also installing the dependencies ‘httpuv’, ‘fontawesome’, ‘sourcetools’, ‘later’, ‘promises’, ‘commonmark’, ‘htmlwidgets’, ‘crosstalk’, ‘numDeriv’, ‘bdsmatrix’, ‘lazyeval’, ‘shiny’, ‘DT’, ‘diffobj’, ‘affyio’, ‘preprocessCore’, ‘plyr’, ‘coda’, ‘bbmle’, ‘irlba’, ‘AnnotationFilter’, ‘ProtGenerics’, ‘interactiveDisplayBase’, ‘sparseMatrixStats’, ‘rhdf5’, ‘rhdf5filters’, ‘Rhdf5lib’, ‘brio’, ‘desc’, ‘pkgload’, ‘praise’, ‘waldo’, ‘affy’, ‘emdbook’, ‘RcppNumerical’, ‘truncnorm’, ‘mixsqp’, ‘SQUAREM’, ‘etrunct’, ‘invgamma’, ‘ensembldb’, ‘AnnotationHub’, ‘Biostrings’, ‘DelayedMatrixStats’, ‘HDF5Array’, ‘beachmat’, ‘testthat’, ‘vsn’, ‘pheatmap’, ‘apeglm’, ‘ashr’, ‘tximport’, ‘tximeta’, ‘tximportData’, ‘pbapply’, ‘airway’, ‘pasilla’, ‘glmGamPoi’

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/httpuv_1.6.6.zip'
Content type 'application/zip' length 1699024 bytes (1.6 MB)
downloaded 1.6 MB

#I deleted some URLs to decrease the characters#

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/windows/contrib/4.1/DESeq2_1.34.0.zip'
Content type 'application/zip' length 2956288 bytes (2.8 MB)
downloaded 2.8 MB

package ‘httpuv’ successfully unpacked and MD5 sums checked
package ‘fontawesome’ successfully unpacked and MD5 sums checked
package ‘sourcetools’ successfully unpacked and MD5 sums checked
package ‘later’ successfully unpacked and MD5 sums checked
package ‘promises’ successfully unpacked and MD5 sums checked
package ‘commonmark’ successfully unpacked and MD5 sums checked
package ‘htmlwidgets’ successfully unpacked and MD5 sums checked
package ‘crosstalk’ successfully unpacked and MD5 sums checked
package ‘numDeriv’ successfully unpacked and MD5 sums checked
package ‘bdsmatrix’ successfully unpacked and MD5 sums checked
package ‘lazyeval’ successfully unpacked and MD5 sums checked
package ‘shiny’ successfully unpacked and MD5 sums checked
package ‘DT’ successfully unpacked and MD5 sums checked
package ‘diffobj’ successfully unpacked and MD5 sums checked
package ‘affyio’ successfully unpacked and MD5 sums checked
package ‘preprocessCore’ successfully unpacked and MD5 sums checked
package ‘plyr’ successfully unpacked and MD5 sums checked
package ‘coda’ successfully unpacked and MD5 sums checked
package ‘bbmle’ successfully unpacked and MD5 sums checked
package ‘irlba’ successfully unpacked and MD5 sums checked
package ‘AnnotationFilter’ successfully unpacked and MD5 sums checked
package ‘ProtGenerics’ successfully unpacked and MD5 sums checked
package ‘interactiveDisplayBase’ successfully unpacked and MD5 sums checked
package ‘sparseMatrixStats’ successfully unpacked and MD5 sums checked
package ‘rhdf5’ successfully unpacked and MD5 sums checked
package ‘rhdf5filters’ successfully unpacked and MD5 sums checked
package ‘Rhdf5lib’ successfully unpacked and MD5 sums checked
package ‘brio’ successfully unpacked and MD5 sums checked
package ‘desc’ successfully unpacked and MD5 sums checked
package ‘pkgload’ successfully unpacked and MD5 sums checked
package ‘praise’ successfully unpacked and MD5 sums checked
package ‘waldo’ successfully unpacked and MD5 sums checked
package ‘affy’ successfully unpacked and MD5 sums checked
package ‘emdbook’ successfully unpacked and MD5 sums checked
package ‘RcppNumerical’ successfully unpacked and MD5 sums checked
package ‘truncnorm’ successfully unpacked and MD5 sums checked
package ‘mixsqp’ successfully unpacked and MD5 sums checked
package ‘SQUAREM’ successfully unpacked and MD5 sums checked
package ‘etrunct’ successfully unpacked and MD5 sums checked
package ‘invgamma’ successfully unpacked and MD5 sums checked
package ‘ensembldb’ successfully unpacked and MD5 sums checked
package ‘AnnotationHub’ successfully unpacked and MD5 sums checked
package ‘Biostrings’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘Biostrings’
Warning: restored ‘Biostrings’
package ‘DelayedMatrixStats’ successfully unpacked and MD5 sums checked
package ‘HDF5Array’ successfully unpacked and MD5 sums checked
package ‘beachmat’ successfully unpacked and MD5 sums checked
package ‘testthat’ successfully unpacked and MD5 sums checked
package ‘vsn’ successfully unpacked and MD5 sums checked
package ‘pheatmap’ successfully unpacked and MD5 sums checked
package ‘apeglm’ successfully unpacked and MD5 sums checked
package ‘ashr’ successfully unpacked and MD5 sums checked
package ‘tximport’ successfully unpacked and MD5 sums checked
package ‘tximeta’ successfully unpacked and MD5 sums checked
package ‘pbapply’ successfully unpacked and MD5 sums checked
package ‘glmGamPoi’ successfully unpacked and MD5 sums checked
package ‘DESeq2’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Masked my real name here\AppData\Local\Temp\1\RtmpIR5YXK\downloaded_packages
installing the source packages ‘tximportData’, ‘airway’, ‘pasilla’

trying URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/tximportData_1.22.0.tar.gz'
Content type 'application/octet-stream' length 426787417 bytes (407.0 MB)
downloaded 407.0 MB

trying URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/airway_1.14.0.tar.gz'
Content type 'application/octet-stream' length 24226937 bytes (23.1 MB)
downloaded 23.1 MB

trying URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/pasilla_1.22.0.tar.gz'
Content type 'application/octet-stream' length 3309386 bytes (3.2 MB)
downloaded 3.2 MB

* installing *source* package 'tximportData' ...
** using staged installation
** inst
** help
No man pages found in package  'tximportData' 
*** installing help indices
** 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 (tximportData)
* installing *source* package 'airway' ...
** using staged installation
** data
** inst
** help
*** installing help indices
  converting help for package 'airway'
    finding HTML links ... done
    airway                                  html  
    gse                                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
Warning: package 'SummarizedExperiment' was built under R version 4.1.1
Warning: package 'MatrixGenerics' was built under R version 4.1.1
Warning: package 'matrixStats' was built under R version 4.1.3
Warning: package 'GenomicRanges' was built under R version 4.1.2
Warning: package 'BiocGenerics' was built under R version 4.1.1
Warning: package 'S4Vectors' was built under R version 4.1.3
Warning: package 'IRanges' was built under R version 4.1.1
Warning: package 'GenomeInfoDb' was built under R version 4.1.2
Warning: package 'Biobase' was built under R version 4.1.1
*** arch - x64
Warning: package 'SummarizedExperiment' was built under R version 4.1.1
Warning: package 'MatrixGenerics' was built under R version 4.1.1
Warning: package 'matrixStats' was built under R version 4.1.3
Warning: package 'GenomicRanges' was built under R version 4.1.2
Warning: package 'BiocGenerics' was built under R version 4.1.1
Warning: package 'S4Vectors' was built under R version 4.1.3
Warning: package 'IRanges' was built under R version 4.1.1
Warning: package 'GenomeInfoDb' was built under R version 4.1.2
Warning: package 'Biobase' was built under R version 4.1.1
** testing if installed package can be loaded from final location
*** arch - i386
Warning: package 'SummarizedExperiment' was built under R version 4.1.1
Warning: package 'MatrixGenerics' was built under R version 4.1.1
Warning: package 'matrixStats' was built under R version 4.1.3
Warning: package 'GenomicRanges' was built under R version 4.1.2
Warning: package 'BiocGenerics' was built under R version 4.1.1
Warning: package 'S4Vectors' was built under R version 4.1.3
Warning: package 'IRanges' was built under R version 4.1.1
Warning: package 'GenomeInfoDb' was built under R version 4.1.2
Warning: package 'Biobase' was built under R version 4.1.1
*** arch - x64
Warning: package 'SummarizedExperiment' was built under R version 4.1.1
Warning: package 'MatrixGenerics' was built under R version 4.1.1
Warning: package 'matrixStats' was built under R version 4.1.3
Warning: package 'GenomicRanges' was built under R version 4.1.2
Warning: package 'BiocGenerics' was built under R version 4.1.1
Warning: package 'S4Vectors' was built under R version 4.1.3
Warning: package 'IRanges' was built under R version 4.1.1
Warning: package 'GenomeInfoDb' was built under R version 4.1.2
Warning: package 'Biobase' was built under R version 4.1.1
** testing if installed package keeps a record of temporary installation path
* DONE (airway)
* installing *source* package 'pasilla' ...
** using staged installation
** data
** inst
** help
*** installing help indices
  converting help for package 'pasilla'
    finding HTML links ... done
    pasillaExons                            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 (pasilla)

The downloaded source packages are in
    ‘C:\Users\Masked my real name here\AppData\Local\Temp\1\RtmpIR5YXK\downloaded_packages’
Installation paths not writeable, unable to update packages
  path: C:/Program Files/R/R-4.1.0/library
  packages:
    class, cluster, foreign, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival
Old packages: 'mnormt', 'RCurl', 'RSQLite', 'stringi', 'XML'
Update all/some/none? [a/s/n]: 
n
Warning messages:
1: In unlink(instPath, recursive = TRUE, force = TRUE) :
  cannot delete reparse point 'C:\Users\Masked my real name here\OneDrive - FDA\Documents\R\win-library\4.1/Biostrings/libs', reason 'There is a mismatch between the tag specified in the request and the tag present in the reparse point'
2: In unlink(instPath, recursive = TRUE) :
  cannot delete reparse point 'C:\Users\Masked my real name here\OneDrive - FDA\Documents\R\win-library\4.1/Biostrings/libs', reason 'There is a mismatch between the tag specified in the request and the tag present in the reparse point'
DESeq2 Install • 4.9k views
ADD COMMENT •
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Entering edit mode
> library(DESeq2)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

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.max, which.min


Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    expand.grid, I, unname

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: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs,
    colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds,
    colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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")'.


Attaching package: ‘Biobase’

The following object is masked from ‘package:MatrixGenerics’:

    rowMedians

The following objects are masked from ‘package:matrixStats’:

    anyMissing, rowMedians

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 ‘Biostrings’
In addition: Warning messages:
1: package ‘DESeq2’ was built under R version 4.1.1 
2: package ‘S4Vectors’ was built under R version 4.1.3 
3: package ‘BiocGenerics’ was built under R version 4.1.1 
4: package ‘IRanges’ was built under R version 4.1.1 
5: package ‘GenomicRanges’ was built under R version 4.1.2 
6: package ‘GenomeInfoDb’ was built under R version 4.1.2 
7: package ‘SummarizedExperiment’ was built under R version 4.1.1 
8: package ‘MatrixGenerics’ was built under R version 4.1.1 
9: package ‘matrixStats’ was built under R version 4.1.3 
10: package ‘Biobase’ was built under R version 4.1.1
ADD REPLY •
0
Entering edit mode
> BiocManager::install("Biostrings",force = TRUE, dependencies = TRUE)
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.0 (2021-05-18)
Installing package(s) 'Biostrings'
also installing the dependencies ‘BSgenome’, ‘BSgenome.Celegans.UCSC.ce2’, ‘BSgenome.Dmelanogaster.UCSC.dm3’, ‘BSgenome.Hsapiens.UCSC.hg18’, ‘drosophila2probe’, ‘hgu95av2probe’, ‘hgu133aprobe’, ‘hgu95av2cdf’, ‘affydata’, ‘RUnit’

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/windows/contrib/4.1/BSgenome_1.62.0.zip'
Content type 'application/zip' length 7698326 bytes (7.3 MB)
downloaded 7.3 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/RUnit_0.4.32.zip'
Content type 'application/zip' length 297385 bytes (290 KB)
downloaded 290 KB

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/windows/contrib/4.1/Biostrings_2.62.0.zip'
Content type 'application/zip' length 14683981 bytes (14.0 MB)
downloaded 14.0 MB

package ‘BSgenome’ successfully unpacked and MD5 sums checked
package ‘RUnit’ successfully unpacked and MD5 sums checked
package ‘Biostrings’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘Biostrings’
Warning: restored ‘Biostrings’

The downloaded binary packages are in
    C:\Users\Masked my real name here\AppData\Local\Temp\1\RtmpIR5YXK\downloaded_packages
installing the source packages ‘BSgenome.Celegans.UCSC.ce2’, ‘BSgenome.Dmelanogaster.UCSC.dm3’, ‘BSgenome.Hsapiens.UCSC.hg18’, ‘drosophila2probe’, ‘hgu95av2probe’, ‘hgu133aprobe’, ‘hgu95av2cdf’, ‘affydata’

trying URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce2_1.4.0.tar.gz'
Content type 'application/octet-stream' length 23653893 bytes (22.6 MB)
downloaded 22.6 MB

trying URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm3_1.4.0.tar.gz'
Content type 'application/octet-stream' length 38546795 bytes (36.8 MB)
downloaded 36.8 MB

#I deleted some URLs#

trying URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/affydata_1.42.0.tar.gz'
Content type 'application/octet-stream' length 12736608 bytes (12.1 MB)
downloaded 12.1 MB
ADD REPLY •
0
Entering edit mode
* installing *source* package 'BSgenome.Celegans.UCSC.ce2' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package 'Biostrings' required by 'BSgenome' could not be found
In addition: Warning messages:
1: package 'BSgenome' was built under R version 4.1.1 
2: package 'BiocGenerics' was built under R version 4.1.1 
3: package 'S4Vectors' was built under R version 4.1.3 
4: package 'IRanges' was built under R version 4.1.1 
5: package 'GenomeInfoDb' was built under R version 4.1.2 
6: package 'GenomicRanges' was built under R version 4.1.2 
Execution halted
ERROR: lazy loading failed for package 'BSgenome.Celegans.UCSC.ce2'
* removing 'C:/Users/Masked my real name here/Documents/R/win-library/4.1/BSgenome.Celegans.UCSC.ce2'
* installing *source* package 'BSgenome.Dmelanogaster.UCSC.dm3' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package 'Biostrings' required by 'BSgenome' could not be found
In addition: Warning messages:
1: package 'BSgenome' was built under R version 4.1.1 
2: package 'BiocGenerics' was built under R version 4.1.1 
3: package 'S4Vectors' was built under R version 4.1.3 
4: package 'IRanges' was built under R version 4.1.1 
5: package 'GenomeInfoDb' was built under R version 4.1.2 
6: package 'GenomicRanges' was built under R version 4.1.2 
Execution halted
ERROR: lazy loading failed for package 'BSgenome.Dmelanogaster.UCSC.dm3'
* removing 'C:/Users/Masked my real name here/Documents/R/win-library/4.1/BSgenome.Dmelanogaster.UCSC.dm3'
* installing *source* package 'BSgenome.Hsapiens.UCSC.hg18' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package 'Biostrings' required by 'BSgenome' could not be found
In addition: Warning messages:
1: package 'BSgenome' was built under R version 4.1.1 
2: package 'BiocGenerics' was built under R version 4.1.1 
3: package 'S4Vectors' was built under R version 4.1.3 
4: package 'IRanges' was built under R version 4.1.1 
5: package 'GenomeInfoDb' was built under R version 4.1.2 
6: package 'GenomicRanges' was built under R version 4.1.2 
Execution halted
ERROR: lazy loading failed for package 'BSgenome.Hsapiens.UCSC.hg18'
* removing 'C:/Users/Masked my real name here/Documents/R/win-library/4.1/BSgenome.Hsapiens.UCSC.hg18'
* installing *source* package 'drosophila2probe' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for 'AnnotationDbi' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'Biostrings'
Error: package 'AnnotationDbi' could not be loaded
In addition: Warning messages:
1: package 'AnnotationDbi' was built under R version 4.1.1 
2: package 'BiocGenerics' was built under R version 4.1.1 
3: package 'Biobase' was built under R version 4.1.1 
4: package 'IRanges' was built under R version 4.1.1 
5: package 'S4Vectors' was built under R version 4.1.3 
Execution halted
ERROR: lazy loading failed for package 'drosophila2probe'
* removing 'C:/Users/Masked my real name here/OneDrive - FDA/Documents/R/win-library/4.1/drosophila2probe'
* installing *source* package 'hgu95av2probe' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for 'AnnotationDbi' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'Biostrings'
Error: package 'AnnotationDbi' could not be loaded
In addition: Warning messages:
1: package 'AnnotationDbi' was built under R version 4.1.1 
2: package 'BiocGenerics' was built under R version 4.1.1 
3: package 'Biobase' was built under R version 4.1.1 
4: package 'IRanges' was built under R version 4.1.1 
5: package 'S4Vectors' was built under R version 4.1.3 
Execution halted
ERROR: lazy loading failed for package 'hgu95av2probe'
* removing 'C:/Users/Masked my real name here/Documents/R/win-library/4.1/hgu95av2probe'
* installing *source* package 'hgu133aprobe' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for 'AnnotationDbi' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'Biostrings'
Error: package 'AnnotationDbi' could not be loaded
In addition: Warning messages:
1: package 'AnnotationDbi' was built under R version 4.1.1 
2: package 'BiocGenerics' was built under R version 4.1.1 
3: package 'Biobase' was built under R version 4.1.1 
4: package 'IRanges' was built under R version 4.1.1 
5: package 'S4Vectors' was built under R version 4.1.3 
Execution halted
ERROR: lazy loading failed for package 'hgu133aprobe'
* removing 'C:/Users/Masked my real name here/Documents/R/win-library/4.1/hgu133aprobe'
* installing *source* package 'hgu95av2cdf' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called 'Biostrings'
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package 'hgu95av2cdf'
* removing 'C:/Users/Masked my real name here/OneDrive - FDA/Documents/R/win-library/4.1/hgu95av2cdf'
* installing *source* package 'affydata' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning messages:
1: package 'affy' was built under R version 4.1.1 
2: package 'BiocGenerics' was built under R version 4.1.1 
3: package 'Biobase' was built under R version 4.1.1 
** help
*** installing help indices
  converting help for package 'affydata'
    finding HTML links ... done
    Dilution                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
Warning: package 'affy' was built under R version 4.1.1
Warning: package 'BiocGenerics' was built under R version 4.1.1
Warning: package 'Biobase' was built under R version 4.1.1
     Package   
[1,] "affydata"
     LibPath                                                                            
[1,] "C:/Users/Masked my real name here/Documents/R/win-library/4.1/00LOCK-affydata/00new"
     Item       Title                        
[1,] "Dilution" "AffyBatch instance Dilution"
*** arch - x64
Warning: package 'affy' was built under R version 4.1.1
Warning: package 'BiocGenerics' was built under R version 4.1.1
Warning: package 'Biobase' was built under R version 4.1.1
     Package   
[1,] "affydata"
     LibPath                                                                            
[1,] "C:/Users/Masked my real name here/R/win-library/4.1/00LOCK-affydata/00new"
     Item       Title                        
[1,] "Dilution" "AffyBatch instance Dilution"
** testing if installed package can be loaded from final location
*** arch - i386
Warning: package 'affy' was built under R version 4.1.1
Warning: package 'BiocGenerics' was built under R version 4.1.1
Warning: package 'Biobase' was built under R version 4.1.1
     Package    LibPath                                                      
[1,] "affydata" "C:/Users/Masked my real name here/OneDrive - FDA/Documents/R/win-library/4.1"
     Item       Title                        
[1,] "Dilution" "AffyBatch instance Dilution"
*** arch - x64
Warning: package 'affy' was built under R version 4.1.1
Warning: package 'BiocGenerics' was built under R version 4.1.1
Warning: package 'Biobase' was built under R version 4.1.1
     Package    LibPath                                                      
[1,] "affydata" "C:/Users/Masked my real name here/Documents/R/win-library/4.1"
     Item       Title                        
[1,] "Dilution" "AffyBatch instance Dilution"
** testing if installed package keeps a record of temporary installation path
* DONE (affydata)

The downloaded source packages are in
    ‘C:\Users\Masked my real name here\AppData\Local\Temp\1\RtmpIR5YXK\downloaded_packages’
Installation paths not writeable, unable to update packages
  path: C:/Program Files/R/R-4.1.0/library
  packages:
    class, cluster, foreign, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival
Old packages: 'mnormt', 'RCurl', 'RSQLite', 'stringi', 'XML'
Update all/some/none? [a/s/n]: 
n
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Warning messages:
1: In unlink(instPath, recursive = TRUE, force = TRUE) :
  cannot delete reparse point 'C:\Users\Masked my real name here\Documents\R\win-library\4.1/Biostrings/libs', reason 'There is a mismatch between the tag specified in the request and the tag present in the reparse point'
2: In unlink(instPath, recursive = TRUE) :
  cannot delete reparse point 'C:\Users\Masked my real name here\Documents\R\win-library\4.1/Biostrings/libs', reason 'There is a mismatch between the tag specified in the request and the tag present in the reparse point'
3: In install.packages(...) :
  installation of package ‘BSgenome.Celegans.UCSC.ce2’ had non-zero exit status
4: In install.packages(...) :
  installation of package ‘BSgenome.Dmelanogaster.UCSC.dm3’ had non-zero exit status
5: In install.packages(...) :
  installation of package ‘BSgenome.Hsapiens.UCSC.hg18’ had non-zero exit status
6: In install.packages(...) :
  installation of package ‘drosophila2probe’ had non-zero exit status
7: In install.packages(...) :
  installation of package ‘hgu95av2probe’ had non-zero exit status
8: In install.packages(...) :
  installation of package ‘hgu133aprobe’ had non-zero exit status
9: In install.packages(...) :
  installation of package ‘hgu95av2cdf’ had non-zero exit status
> library(DESeq2)
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 ‘Biostrings’
In addition: Warning message:
package ‘DESeq2’ was built under R version 4.1.1
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I am new to R. I am using a work computer so I cannot change any installed software unless with the administrative right from the IT side. It is easier for me not to change the current R version in Rstudio ( 4.1.0.) I installed the matched version BioManager (3.14). It looks like I installed everything or maybe not. I cannot use DESeq2. I also do not have Rtools installed if this is an issue. Any help is appreciated. Thank you!!!

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@james-w-macdonald-5106
Last seen 10 minutes ago
United States

The critical part of all that (!) is these three lines:

package ‘Biostrings’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘Biostrings’
Warning: restored ‘Biostrings’

Which basically says that you cannot install Biostrings because you cannot first remove the existing version. There are several reasons why this may be so. You might have another instance of R running that has Biostrings loaded. You might already have Biostrings loaded in your current R session. You may have a partially installed version of the package.

Anyway, it looks like it might be broken somehow, so try quitting all R instances you have running, then restart and try installing just Biostrings. If it still fails, you can restart and try doing

remove.packages("Biostrings")

And then try to install the package. That will likely fail, but give it a try. As a final alternative, you can figure out where it's installed

installed.packages()["Biostrings","LibPath"]

And then quit R, go to that directory and delete the Biostrings subdirectory, and any directory that has 00LOCK in the name. Then restart R, and try to install Biostrings again.
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Hi James, thanks for your time. I tried in the old project and newly created project:

> remove.packages("Biostrings")
Removing package from ‘C:/Users/my name/Documents/R/win-library/4.1’
(as ‘lib’ is unspecified)
Error in remove.packages : there is no package called ‘Biostrings’

> installed.packages()["Biostrings","LibPath"]
Error in installed.packages()["Biostrings", "LibPath"] : 
  subscript out of bounds

For the local files, I 100% saw the Biostrings folder, when I tried to delete is manually, I cannot do anything. When I access to the folder, the pop-up window says: the location is not available: C:\Users\My name\Documents\R\win-library\4.1\Biostrings\libs is not accessible. The tag present in the reparse point buffer is invalid. I searched about this error message and it looks like it is a Onedrive bug. I will try to fix this first... Thank you.

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Wait. Are you installing your packages on a OneDrive location? It doesn't look like one, but if so, that is probably suboptimal. On my Win10 box it uses this path

> .libPaths()
[1] "C:/Users/jmacdon/AppData/Local/R/win-library/4.2"
[2] "C:/Program Files/R/R-4.2.0/library"

Which is good because A) no spaces in the path, which can be problematic sometimes, and B) it's local and not subject to being synchronized with a cloud location.

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Also, there won't be anything at C:\Users\My name\Documents\R\win-library\4.1\Biostrings\libs. The directory you are looking for is C:\Users\My name\Documents\R\win-library\4.1\Biostrings

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Thank you! I indeed somehow have library in Onedrive. I hide my name and one drive in the previous post. My path:

> .libPaths()
[1] "C:/Users/My name/OneDrive/Documents/R/win-library/4.1" "C:/Program Files/R/R-4.1.0/library"

Only libs folder exsit in Biostrings now. My cloud record showed more folders in Biostrings in August. I am trying to either install packages in a public available folder or get some IT help with Onedrive.

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Just don't use your OneDrive folder to install packages. There's no good reason to do so, and I can come up with multiple reasons not to. If I were you I would switch to using the AppData/Local/R/win-library/ directory.

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I cannot bypass OneDrive unfortunately. Except the software, everything is syned.

Would it work if I use this every time:

myPaths <- .libPaths()

myPaths <- c(myPaths, "C:/Users/Public/AppData/Local/R/win-library/4.1")

.libPaths(myPaths)
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It looks like it won't work.

> myPaths <- .libPaths()
> myPaths <- c(myPaths, "C:/Users/Public/AppData/Local/R/win-library/4.1")
> .libPaths(myPaths) 

> if("DESeq2" %in% installed.packages()[,1]) remove.packages("DESeq2")
Removing package from ‘C:/Users/my name/OneDrive/Documents/R/win-library/4.1’
(as ‘lib’ is unspecified)
> if("BioManager" %in% installed.packages()[,1]) remove.packages("BioManager")
> if("Biostrings" %in% installed.packages()[,1]) remove.packages("Biostrings")
> if (!require("BiocManager", quietly = TRUE))
+   install.packages("BiocManager")

Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.0 (2021-05-18)
Bioconductor version '3.14' is out-of-date; the current release version '3.15' is available with R version '4.2'; see
  https://bioconductor.org/install
Warning message:
package ‘BiocManager’ was built under R version 4.1.3 
> BiocManager::install(version = "3.14", force = TRUE, dependencies = TRUE)
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.0 (2021-05-18)
Installation paths not writeable, unable to update packages
  path: C:/Program Files/R/R-4.1.0/library
  packages:
    class, cluster, foreign, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival
Old packages: 'mnormt', 'RCurl', 'RSQLite', 'stringi', 'XML'
Update all/some/none? [a/s/n]:

But somehow in the Tools->install package, I can use this path "C:/Users/Public/AppData/Local/R/win-library/4.1" now. Then I need to figure out how to install packages this way...

> install.packages("BiocManager", lib="C:/Users/Public/AppData/Local/R/win-library/4.1")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/BiocManager_1.30.18.zip'
Content type 'application/zip' length 361140 bytes (352 KB)
downloaded 352 KB

package ‘BiocManager’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\my name\AppData\Local\Temp\1\RtmpwPKlmU\downloaded_packages
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Biocmanager seems worked. But not for the DESeq2 and Biostrings due to version issue:

> install.packages("DESeq2", lib="C:/Users/Public/AppData/Local/R/win-library/4.1")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/
Warning in install.packages :
  package ‘DESeq2’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
> install.packages("Biostrings", lib="C:/Users/Public/AppData/Local/R/win-library/4.1")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/
Warning in install.packages :
  package ‘Biostrings’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
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Is there a way to install the older version of DESeq2? Thanks!

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The version of BiocManager you have installed will install the correct version of DESeq. If you want other versions (you should have a good reason for this), you will need to install the version of R that is matched with that version of DESeq2. In general you should run the current release versions of R and Bioconductor, as we do not support anything else.

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(A) Previously, to match the version of R 4.1.0 (2021-05-18), I specifically install BiocManager version 3.14 by using code:

BiocManager::install(version = "3.14", force = TRUE, dependencies = TRUE)

I am not sure if this is the right thing to do. Maybe with R 4.1.0, I can still use the lastest version of DESeq2, right?

(B) If I delete the old Biostrings folder and reinstall, do you think it will solve this problem? I cannot change the default path where the packages were stored without administrative right. If I change path manully with code every time, will it help with the installation? Like this:

myPaths <- .libPaths()
myPaths <- c(myPaths, "C:/Users/Public/AppData/Local/R/win-library/4.1")
.libPaths(myPaths) 
BiocManager::install("DESeq2",force = TRUE, dependencies = TRUE)

```

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R-4.1.0 works with both Bioconductor 3.13 and 3.14, and those are the only two versions you will be able to specify. We are now on 3.15, and will soon be on 3.16. So you are rapidly getting out of date.

Deleting the old Biostrings folder and re-installing was one of the suggestions I already made, so yes I think it may help. But in general you may have problems with a directory that is being synced to cloud locations. I have never done that, so I can't say for sure. But I'm putting it out there.

If you cannot change the library directory location, I would try deleting and installing first.

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Sorry to bother you yesterday. I was trying to trouble shoot by myself. I should have contacted IT earlier. For anyone who experienced the same problem (computer with cloud storage and lack of admin right), I reinstalled R and RStudio and changed the path (not using default path C:/ Program Files). Thanks to the reinstallation, I use the latest version R version 4.2.1 (2022-06-23 ucrt) now. And I am able to install everything easily.

I found one article that may be useful: "Changing the Default Library in Rstudio to a Different Default Library (Temporary)" https://www.accelebrate.com/library/how-to-articles/r-rstudio-library

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Glad to hear you got it fixed!

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