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Question: Installation problem, S4Vectors, something about "apply_hotfix73465" not found
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gravatar for dchmiller
9 weeks ago by
dchmiller0
dchmiller0 wrote:

I'm trying to install "S4Vectors" with "biocLite()", and it fails. Full feedback at bottom, relevant bit here:

Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’
Creating a new generic function for ‘expand.grid’ in package ‘S4Vectors’
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : 
  object 'apply_hotfix73465' not found
Error : unable to load R code in package ‘S4Vectors’
ERROR: lazy loading failed for package ‘S4Vectors’

I would appreciate if anyone can steer me towards how to troubleshoot this.

Does anyone know what "apply_hotfix73465" is? I didn't see any posts, or anything on web search, about this kind of error. I am assuming it's something inside of "S4Vectors", and I'm somehow not providing it. How to I obtain this hotfix?

- Darach Miller @ NYU

R> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help
R> biocLite("S4Vectors")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).
Installing package(s) ‘S4Vectors’
trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/S4Vectors_0.14.7.tar.gz'
Content type 'application/x-gzip' length 430115 bytes (420 KB)
==================================================
downloaded 420 KB

NULL
* installing *source* package ‘S4Vectors’ ...
** libs
gcc -I/usr/include/R/ -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt  -c AEbufs.c -o AEbufs.o
gcc -I/usr/include/R/ -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt  -c DataFrame_class.c -o DataFrame_class.o
gcc -I/usr/include/R/ -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt  -c Hits_class.c -o Hits_class.o
gcc -I/usr/include/R/ -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt  -c Linteger_class.c -o Linteger_class.o
gcc -I/usr/include/R/ -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt  -c List_class.c -o List_class.o
gcc -I/usr/include/R/ -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt  -c R_init_S4Vectors.c -o R_init_S4Vectors.o
gcc -I/usr/include/R/ -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt  -c Rle_class.c -o Rle_class.o
gcc -I/usr/include/R/ -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt  -c Rle_utils.c -o Rle_utils.o
gcc -I/usr/include/R/ -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt  -c SEXP_utils.c -o SEXP_utils.o
gcc -I/usr/include/R/ -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt  -c SimpleList_class.c -o SimpleList_class.o
gcc -I/usr/include/R/ -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt  -c anyMissing.c -o anyMissing.o
gcc -I/usr/include/R/ -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt  -c eval_utils.c -o eval_utils.o
gcc -I/usr/include/R/ -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt  -c hash_utils.c -o hash_utils.o
gcc -I/usr/include/R/ -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt  -c int_utils.c -o int_utils.o
gcc -I/usr/include/R/ -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt  -c logical_utils.c -o logical_utils.o
gcc -I/usr/include/R/ -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt  -c map_ranges_to_runs.c -o map_ranges_to_runs.o
gcc -I/usr/include/R/ -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt  -c safe_arithm.c -o safe_arithm.o
gcc -I/usr/include/R/ -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt  -c sort_utils.c -o sort_utils.o
gcc -I/usr/include/R/ -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt  -c str_utils.c -o str_utils.o
gcc -I/usr/include/R/ -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt  -c subsetting_utils.c -o subsetting_utils.o
gcc -I/usr/include/R/ -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt  -c vector_utils.c -o vector_utils.o
gcc -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o Linteger_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o eval_utils.o hash_utils.o int_utils.o logical_utils.o map_ranges_to_runs.o safe_arithm.o sort_utils.o str_utils.o subsetting_utils.o vector_utils.o -L/usr/lib64/R/lib -lR
installing to /home/zed/R/x86_64-pc-linux-gnu-library/3.4/S4Vectors/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’
Creating a new generic function for ‘expand.grid’ in package ‘S4Vectors’
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : 
  object 'apply_hotfix73465' not found
Error : unable to load R code in package ‘S4Vectors’
ERROR: lazy loading failed for package ‘S4Vectors’
* removing ‘/home/zed/R/x86_64-pc-linux-gnu-library/3.4/S4Vectors’

The downloaded source packages are in
	‘/tmp/RtmpnNF29d/downloaded_packages’
installation path not writeable, unable to update packages: boot, Matrix, mgcv
Old packages: 'backports', 'BiocGenerics', 'chron', 'curl', 'doParallel',
  'ggrepel', 'limma', 'lme4', 'magick'
Update all/some/none? [a/s/n]: n
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘S4Vectors’ had non-zero exit status
R> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux

Matrix products: default
BLAS: /usr/lib/libblas.so.3.7.1
LAPACK: /usr/lib/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] 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   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] 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_1.26.1

loaded via a namespace (and not attached):
[1] compiler_3.4.1 tools_3.4.1  
ADD COMMENTlink modified 9 weeks ago by Martin Morgan ♦♦ 21k • written 9 weeks ago by dchmiller0
1
gravatar for Martin Morgan
9 weeks ago by
Martin Morgan ♦♦ 21k
United States
Martin Morgan ♦♦ 21k wrote:

One of your packages (probably BiocGenerics) is out-of-date with respect to others. Try

BiocInstaller::biocValid()

and follow any recommendations it has.

ADD COMMENTlink written 9 weeks ago by Martin Morgan ♦♦ 21k

It seems to have fixed itself!

I started to try the biocValid() call, but first re-tried the installation of S4Vectors. It worked, which suprised me, until I ran sessionInfo:

R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux

Matrix products: default
BLAS: /usr/lib/libblas.so.3.7.1
LAPACK: /usr/lib/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] 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   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] 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_1.26.1

loaded via a namespace (and not attached):
[1] compiler_3.4.2 tools_3.4.2

It would appear that my R was upgraded somehow from 3.4.1 to 3.4.2 . I don't know how, as I didn't ask for an upgrade and had rebooted my system before testing biocLite("S4Vectors") the first time ( with a failed install ). I have not rebooted since then, and then it works. Very weird, and sort of disturbing ( am I sleep-upgrading?!?! ). I believe the problem is that my libraries were somehow halfway upgraded and out-of-date.

For records, the command it originally choked on was

Creating a generic function for ‘%in%’ from package ‘base’ in package ‘S4Vectors’

Everything works now. Thanks for the pointer!

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by dchmiller0
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