biocLite updating problem with Ubuntu 17.10
2
0
Entering edit mode
KRA • 0
@kra-12378
Last seen 4.8 years ago

Hello,

I am trying to use biocLite to get few packages, but I am unable to use biocLite().

I have tried removing and installing BiocGenerics and also tried  root instaling biocgenerics using

 sudo apt-get install r-bioc-biocgenerics.Even then, I was unable to update the packages.

After using 

source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.2 (2017-09-28).
Installing package(s) ‘IRanges’, ‘AnnotationDbi’
also installing the dependencies ‘BiocGenerics’, ‘S4Vectors’

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/BiocGenerics_0.24.0.tar.gz'
Content type 'application/x-gzip' length 43393 bytes (42 KB)
==================================================
downloaded 42 KB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/S4Vectors_0.16.0.tar.gz'
Content type 'application/x-gzip' length 432152 bytes (422 KB)
==================================================
downloaded 422 KB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/IRanges_2.12.0.tar.gz'
Content type 'application/x-gzip' length 485066 bytes (473 KB)
==================================================
downloaded 473 KB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/AnnotationDbi_1.40.0.tar.gz'
Content type 'application/x-gzip' length 4336842 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

* installing *source* package ‘BiocGenerics’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘append’ in package ‘BiocGenerics’
Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’
Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’
Error : identical(as.call(parse(text = old_code)[[1L]]), body[[7L]][[3L]]) is not TRUE
Error in apply_hotfix73465(getGeneric("cbind")) : 
  hotfix failed for generic function cbind()
Error : unable to load R code in package ‘BiocGenerics’
ERROR: lazy loading failed for package ‘BiocGenerics’
* removing ‘/home/kishore/R/x86_64-pc-linux-gnu-library/3.4/BiocGenerics’
* installing *source* package ‘S4Vectors’ ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c AEbufs.c -o AEbufs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c DataFrame_class.c -o DataFrame_class.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Hits_class.c -o Hits_class.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c LLint_class.c -o LLint_class.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c List_class.c -o List_class.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_S4Vectors.c -o R_init_S4Vectors.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Rle_class.c -o Rle_class.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Rle_utils.c -o Rle_utils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SEXP_utils.c -o SEXP_utils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SimpleList_class.c -o SimpleList_class.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c character_utils.c -o character_utils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c eval_utils.c -o eval_utils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c hash_utils.c -o hash_utils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c integer_utils.c -o integer_utils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c logical_utils.c -o logical_utils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c map_ranges_to_runs.c -o map_ranges_to_runs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c safe_arithm.c -o safe_arithm.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sort_utils.c -o sort_utils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c subsetting_utils.c -o subsetting_utils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c vector_utils.c -o vector_utils.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o -L/usr/lib/R/lib -lR
installing to /home/kishore/R/x86_64-pc-linux-gnu-library/3.4/S4Vectors/libs
** R
** inst
** preparing package for lazy loading
Error : package ‘BiocGenerics’ 0.22.1 was found, but >= 0.23.3 is required by ‘S4Vectors’
ERROR: lazy loading failed for package ‘S4Vectors’
* removing ‘/home/kishore/R/x86_64-pc-linux-gnu-library/3.4/S4Vectors’
ERROR: dependency ‘S4Vectors’ is not available for package ‘IRanges’
* removing ‘/home/kishore/R/x86_64-pc-linux-gnu-library/3.4/IRanges’
ERROR: dependencies ‘IRanges’, ‘S4Vectors’ are not available for package ‘AnnotationDbi’
* removing ‘/home/kishore/R/x86_64-pc-linux-gnu-library/3.4/AnnotationDbi’

The downloaded source packages are in
	‘/tmp/RtmpV4vLzE/downloaded_packages’
installation path not writeable, unable to update packages: BiocGenerics
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘BiocGenerics’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘S4Vectors’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘IRanges’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘AnnotationDbi’ had non-zero exit status

 

# Session Info 

sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 17.10

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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

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

other attached packages:
[1] BiocInstaller_1.28.0

loaded via a namespace (and not attached):
 [1] igraph_1.1.2       hash_2.2.6         Rcpp_0.12.14       magrittr_1.5       bit_1.1-12         rlang_0.1.4       
 [7] blob_1.1.0         plyr_1.8.4         caTools_1.17.1     tools_3.4.2        png_0.1-7          plotrix_3.7       
[13] KernSmooth_2.23-15 DBI_0.7            STRINGdb_1.18.0    gtools_3.5.0       yaml_2.1.16        digest_0.6.13     
[19] bit64_0.9-7        tibble_1.3.4       RColorBrewer_1.1-2 bitops_1.0-6       RCurl_1.95-4.8     memoise_1.1.0     
[25] RSQLite_2.0        gsubfn_0.6-6       gdata_2.18.0       compiler_3.4.2     gplots_3.0.1       chron_2.3-51      
[31] sqldf_0.4-11       proto_1.0.0        pkgconfig_2.0.1

 
ubuntu biocgenerics s4vectors IRanges annotationdbi • 2.5k views
ADD COMMENT •
1
Entering edit mode
@martin-morgan-1513
Last seen 10 hours ago
United States

The release R-3-4-2 contained a bug. BiocGenerics is trying to fix the bug 'on the fly'. The bug fix fails, probably because the user who installed R is different from the user who is trying to patch it.

* installing *source* package ‘BiocGenerics’ ...
...
Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’
Error : identical(as.call(parse(text = old_code)[[1L]]), body[[7L]][[3L]]) is not TRUE
Error in apply_hotfix73465(getGeneric("cbind")) : 
  hotfix failed for generic function cbind()
Error : unable to load R code in package ‘BiocGenerics’
ERROR: lazy loading failed for package ‘BiocGenerics’

I think the alternatives are (a) to install the current version of R, version 3.4.3; or (b) to install the current version of BiocGenerics as the same user used to install R. I think your use of biocLite() fails because the version of BiocGenerics installed by sudo apt ... is older than the currently available version, so biocLite() (run as non-sudo) tries to install an updated version.

 
ADD COMMENT •
0
Entering edit mode

Thank You Martin !!

I have upgraded to 3.4.3 and it fixed the problem.

ADD REPLY •
0
Entering edit mode
@james-w-macdonald-5106
Last seen 10 hours ago
United States

You should probably do

biocValid()

and follow the instructions you get.
ADD COMMENT •
0
Entering edit mode

Hello James,

I tried to downgrade as per `biocValid()` instructions, but it will still giving me the errors.

ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 485 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