library(HTSFilter) says that "HTSFilter" does not exist
2
0
Entering edit mode
Ian • 0
@Ian-24386
Last seen 3.9 years ago

Enter the body of text here

When I try and load the HTSFilter library, I get a message saying that it does not exist. When I try to reinstall the HTSFilter package, I get an error saying that I need the DESeq package, which is not compatible with my version of R (4.0.3). HTSFilter was working for me last week before I updated a bunch of R packages. This is also all being done on the cloud.

Code should be placed in three backticks as shown below

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("HTSFilter")

-Output:
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'HTSFilter'
trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/HTSFilter_1.30.0.tar.gz'
Content type 'application/x-gzip' length 561765 bytes (548 KB)
==================================================
downloaded 548 KB

* installing *source* package ‘HTSFilter’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘DESeq’ was installed before R 4.0.0: please re-install it
Execution halted
ERROR: lazy loading failed for package ‘HTSFilter’
* removing ‘/usr/local/lib/R/site-library/HTSFilter’

The downloaded source packages are in
    ‘/tmp/Rtmpbk1u49/downloaded_packages’
Old packages: 'cellHTS2', 'RMariaDB', 'htmlwidgets', 'rgl', 'nlme'
Update all/some/none? [a/s/n]: 
a
trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/cellHTS2_2.54.0.tar.gz'
Content type 'application/x-gzip' length 3201592 bytes (3.1 MB)
==================================================
downloaded 3.1 MB

trying URL 'https://cloud.r-project.org/src/contrib/RMariaDB_1.0.10.tar.gz'
Content type 'application/x-gzip' length 45906 bytes (44 KB)
==================================================
downloaded 44 KB

* installing *source* package ‘cellHTS2’ ...
mv: cannot move '/usr/local/lib/R/site-library/cellHTS2' to '/usr/local/lib/R/site-library/00LOCK-cellHTS2/cellHTS2': Permission denied
ERROR: cannot remove earlier installation, is it in use?
* removing ‘/usr/local/lib/R/site-library/cellHTS2’
* installing *source* package ‘RMariaDB’ ...
** package ‘RMariaDB’ successfully unpacked and MD5 sums checked
mv: cannot move '/usr/local/lib/R/site-library/RMariaDB' to '/usr/local/lib/R/site-library/00LOCK-RMariaDB/RMariaDB': Permission denied
ERROR: cannot remove earlier installation, is it in use?
* removing ‘/usr/local/lib/R/site-library/RMariaDB’

The downloaded source packages are in
    ‘/tmp/Rtmpbk1u49/downloaded_packages’
trying URL 'https://cloud.r-project.org/src/contrib/htmlwidgets_1.5.3.tar.gz'
Content type 'application/x-gzip' length 323656 bytes (316 KB)
==================================================
downloaded 316 KB

trying URL 'https://cloud.r-project.org/src/contrib/rgl_0.103.5.tar.gz'
Content type 'application/x-gzip' length 3386922 bytes (3.2 MB)
==================================================
downloaded 3.2 MB

* installing *source* package ‘htmlwidgets’ ...
** package ‘htmlwidgets’ successfully unpacked and MD5 sums checked
mv: cannot move '/usr/lib/R/site-library/htmlwidgets' to '/usr/lib/R/site-library/00LOCK-htmlwidgets/htmlwidgets': Permission denied
ERROR: cannot remove earlier installation, is it in use?
* removing ‘/usr/lib/R/site-library/htmlwidgets’
* installing *source* package ‘rgl’ ...
** package ‘rgl’ successfully unpacked and MD5 sums checked
mv: cannot move '/usr/lib/R/site-library/rgl' to '/usr/lib/R/site-library/00LOCK-rgl/rgl': Permission denied
ERROR: cannot remove earlier installation, is it in use?
* removing ‘/usr/lib/R/site-library/rgl’

The downloaded source packages are in
    ‘/tmp/Rtmpbk1u49/downloaded_packages’
trying URL 'https://cloud.r-project.org/src/contrib/nlme_3.1-151.tar.gz'
Content type 'application/x-gzip' length 805592 bytes (786 KB)
==================================================
downloaded 786 KB

* installing *source* package ‘nlme’ ...
** package ‘nlme’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong  -c chol.f -o chol.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c corStruct.c -o corStruct.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gnls.c -o gnls.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c matrix.c -o matrix.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nlOptimizer.c -o nlOptimizer.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nlme.c -o nlme.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nlmefit.c -o nlmefit.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pdMat.c -o pdMat.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pythag.c -o pythag.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong  -c rs.f -o rs.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o pdMat.o pythag.o rs.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /usr/lib/R/library/00LOCK-nlme/00new/nlme/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘lattice’ was installed before R 4.0.0: please re-install it
Execution halted
ERROR: lazy loading failed for package ‘nlme’
* removing ‘/usr/lib/R/library/nlme’
* restoring previous ‘/usr/lib/R/library/nlme’

The downloaded source packages are in
    ‘/tmp/Rtmpbk1u49/downloaded_packages’
Updating HTML index of packages in '.Library'
Warning messages:
1: In install.packages(...) :
  installation of package ‘HTSFilter’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘cellHTS2’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘RMariaDB’ had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘htmlwidgets’ had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘rgl’ had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘nlme’ had non-zero exit status
7: In file.create(f.tg) :
  cannot create file '/usr/share/R/doc/html/packages.html', reason 'Permission denied'
8: In make.packages.html(.Library) : cannot update HTML package index

library(HTSFilter)

-Output:
Error in library(HTSFilter) : there is no package called ‘HTSFilter’

include your problematic code here with any corresponding output

please also include the results of running the following in an R session

sessionInfo( )

-Output: R version 4.0.3 (2020-10-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.5 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

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

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

other attached packages: [1] locfit_1.5-9.4 sva_3.38.0 mgcv_1.8-33
[4] nlme_3.1-151 BiocParallel_1.24.1 Hmisc_4.4-2
[7] ggplot2_3.3.2 Formula_1.2-4 survival_3.2-7
[10] lattice_0.20-41 edgeR_3.32.0 limma_3.46.0
[13] vsn_3.58.0 genefilter_1.72.0 RColorBrewer_1.1-2
[16] gplots_3.1.1 dplyr_1.0.2 biomaRt_2.46.0
[19] DESeq2_1.30.0 SummarizedExperiment_1.20.0 Biobase_2.50.0
[22] MatrixGenerics_1.2.0 matrixStats_0.57.0 GenomicRanges_1.42.0
[25] GenomeInfoDb_1.26.2 IRanges_2.24.1 S4Vectors_0.28.1
[28] BiocGenerics_0.36.0

loaded via a namespace (and not attached): [1] colorspace_2.0-0 ellipsis_0.3.1 rprojroot_2.0.2 rsconnect_0.8.16
[5] htmlTable_2.1.0 XVector_0.30.0 base64enc_0.1-3 rstudioapi_0.13
[9] affyio_1.60.0 bit64_4.0.5 fansi_0.4.1 AnnotationDbi_1.52.0
[13] xml2_1.3.2 splines_4.0.3 geneplotter_1.68.0 knitr_1.30
[17] pkgload_1.1.0 annotate_1.68.0 cluster_2.1.0 dbplyr_2.0.0
[21] png_0.1-7 BiocManager_1.30.10 compiler_4.0.3 httr_1.4.2
[25] backports_1.2.1 assertthat_0.2.1 Matrix_1.2-18 cli_2.2.0
[29] htmltools_0.5.0 prettyunits_1.1.1 tools_4.0.3 gtable_0.3.0
[33] glue_1.4.2 GenomeInfoDbData_1.2.4 affy_1.68.0 rappdirs_0.3.1
[37] Rcpp_1.0.5 vctrs_0.3.5 preprocessCore_1.52.0 xfun_0.19
[41] stringr_1.4.0 testthat_3.0.0 lifecycle_0.2.0 gtools_3.8.2
[45] XML_3.99-0.5 zlibbioc_1.36.0 scales_1.1.1 hms_0.5.3
[49] yaml_2.2.1 curl_4.3 memoise_1.1.0 gridExtra_2.3
[53] rpart_4.1-15 latticeExtra_0.6-29 stringi_1.5.3 RSQLite_2.2.1
[57] desc_1.2.0 checkmate_2.0.0 caTools_1.18.0 rlang_0.4.9
[61] pkgconfig_2.0.3 bitops_1.0-6 purrr_0.3.4 htmlwidgets_1.5.3
[65] bit_4.0.4 tidyselect_1.1.0 magrittr_2.0.1 R6_2.5.0
[69] generics_0.1.0 DelayedArray_0.16.0 DBI_1.1.0 pillar_1.4.7
[73] foreign_0.8-80 withr_2.3.0 RCurl_1.98-1.2 nnet_7.3-14
[77] tibble_3.0.4 crayon_1.3.4 KernSmooth_2.23-18 BiocFileCache_1.14.0
[81] jpeg_0.1-8.1 progress_1.2.2 grid_4.0.3 data.table_1.13.4
[85] blob_1.2.1 digest_0.6.27 xtable_1.8-4 openssl_1.4.3
[89] munsell_0.5.0 sessioninfo_1.1.1 askpass_1.1 ```
DESeq2 HTSFilter • 1.8k views
ADD COMMENT •
1
Entering edit mode
@james-w-macdonald-5106
Last seen 34 minutes ago
United States

Try restarting R, then do

library(BiocManager)
valid()

And then do whatever it tells you to do.
ADD COMMENT •
0
Entering edit mode

This is the output that I get for that:

Bioconductor version '3.12'

  • 4 packages out-of-date
  • 0 packages too new

create a valid installation with

BiocManager::install(c( "cellHTS2", "htmlwidgets", "rgl", "RMariaDB" ), update = TRUE, ask = FALSE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning message: 4 packages out-of-date; 0 packages too new

However, when I run this it turns out that I need to update the "lattice" package, which seems to be the root of my problems, but R won't let me do it because I need to uninstall "lattice" package before I can update it.

ADD REPLY •
0
Entering edit mode

The lattice package prompts me to update it, but when I try it gets me in a loop of asking to restart R. If I choose to not restart R I get an error message:

Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) trying URL 'https://cloud.r-project.org/src/contrib/lattice_0.20-41.tar.gz'

Content type 'application/x-gzip' length 389631 bytes (380 KB)

downloaded 380 KB

  • installing source package ‘lattice’ ... ** package ‘lattice’ successfully unpacked and MD5 sums checked mv: cannot move '/usr/local/lib/R/site-library/lattice' to '/usr/local/lib/R/site-library/00LOCK-lattice/lattice': Permission denied ERROR: cannot remove earlier installation, is it in use?
  • removing ‘/usr/local/lib/R/site-library/lattice’ Warning in install.packages : installation of package ‘lattice’ had non-zero exit status

The downloaded source packages are in ‘/tmp/RtmptoksD4/downloaded_packages’ Warning in install.packages : converting NULL pointer to R NULL

The lattice package is not in use, but this always comes up.

ADD REPLY •
0
Entering edit mode

OK. Try quitting R and then going to /usr/local/lib/R/site-library/ and deleting any directory that starts with 00LOCK. Then try again.

ADD REPLY •
1
Entering edit mode
andrea.rau ▴ 80
@andrearau-7032
Last seen 2.6 years ago
INRAE / Jouy en Josas, France

Hello,

I had forgotten to remove a trailing unnecessary dependency on DESeq in HTSFilter until very recently, and since DESeq was deprecated starting in Bioconductor v3.12, that was causing the installation problem for HTSFilter in R >v4.0. I've removed that dependency and you can install HTSFilter either using the development version of Bioconductor (which requires R v4.1) or directly from my GitHub for R v4.0.x repo using devtools::install_github("andreamrau/HTSFilter").

Best, AR
ADD COMMENT •
0
Entering edit mode

Thanks for that helpful information Andrea. Unfortunately I am still getting an error saying I cannot update the HTSFilter package. Note that even though I only updated the CRAN packages here I also tried to update All and got the same result as shown here.

devtools::install_github("andreamrau/HTSFilter") Downloading GitHub repo andreamrau/HTSFilter@HEAD These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?

1: All
2: CRAN packages only
3: None
4: pkgbuild (1.1.0 -> 1.2.0) [CRAN]

Enter one or more numbers, or an empty line to skip updates:2 pkgbuild (1.1.0 -> 1.2.0) [CRAN] Installing 1 packages: pkgbuild Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) trying URL 'https://cloud.r-project.org/src/contrib/pkgbuild_1.2.0.tar.gz'

Content type 'application/x-gzip' length 30383 bytes (29 KB)

downloaded 29 KB

  • installing source package ‘pkgbuild’ ... ** package ‘pkgbuild’ successfully unpacked and MD5 sums checked mv: cannot move '/usr/local/lib/R/site-library/pkgbuild' to '/usr/local/lib/R/site-library/00LOCK-pkgbuild/pkgbuild': Permission denied ERROR: cannot remove earlier installation, is it in use?
  • removing ‘/usr/local/lib/R/site-library/pkgbuild’ Error: Failed to install 'HTSFilter' from GitHub: (converted from warning) installation of package ‘pkgbuild’ had non-zero exit status
ADD REPLY •
0
Entering edit mode

Looks like a similar issue that James W. MacDonald mentioned a fix for above, notably that the pkgdown package (which is needed by devtools for the installation from GitHub) has an issue with permissions. Try closing R, navigating to /usr/local/lib/R/site-library/ and deleting the directory 00LOCK-pkgbuild, and starting again.

As a side note, I pushed a bug fix to the release version of HTSFilter (v1.30.1) on Bioconductor, but it will probably take a day or two to propagate to the site.

ADD REPLY •
0
Entering edit mode

I was able to get it to work by selection option 3 instead of option 1 or 2. Thank you so much Andrea!

ADD REPLY •
0
Entering edit mode

Great, glad to hear it! AR

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