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 2 days 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

ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 802 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6