Question: how install the package EBIamge on the software R 3.3.1?
1
gravatar for jeankarlosbarrosgalote
2.6 years ago by
jeankarlosbarrosgalote10 wrote:

Hi, everyone!

 

 can not run the EBImage package in R version 3.3.1 software, the following error post:

require (EBImage)
Loading required package: EBImage
Error in get (Info [i, 1], envir = env):
   lazy-load database 'C: /Users/Gean/Documents/R/win-library/3.3/abind/R/abind.rdb' is corrupt
In addition: Warning message:
In get (Info [i, 1], envir = env): internal error -3 in R_decompress1

I've used the following commands:

remove.packages ('abind')
remove.packages ("BiocInstaller")

source ("https://bioconductor.org/biocLite.R")

biocLite ("EBImage")
biocLite ('abind')

but still has the same error

 

ebimage R • 811 views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by jeankarlosbarrosgalote10

Make sure that abind is really removed, that is, that there is no directory 'abind' in the directories pointed to by .libPaths(). You might need to remove it using your operating system. Once it is really removed, try biocLite('abind') again.

ADD REPLYlink written 2.6 years ago by Martin Morgan ♦♦ 23k

Hi,

I have uninstalled, the software, R also Rstudio, and again downloaded the CRAN base, also this deleted files, in library.

but this error appears again:

 

> source("https://bioconductor.org/biocLite.R")
Installing package into ‘C:/Users/Gean/Documents/R/win-library/3.3’
(as ‘lib’ is unspecified)
trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/BiocInstaller_1.22.3.zip'
Content type 'application/zip' length 119756 bytes (116 KB)
downloaded 116 KB

package ‘BiocInstaller’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Gean\AppData\Local\Temp\RtmpEnNb2N\downloaded_packages
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
> biocLite("EBImage")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.0 (2016-05-03).
Installing package(s) ‘EBImage’
also installing the dependencies ‘BiocGenerics’, ‘abind’

trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/BiocGenerics_0.18.0.zip'
Content type 'application/zip' length 966930 bytes (944 KB)
downloaded 944 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/abind_1.4-5.zip'
Content type 'application/zip' length 40195 bytes (39 KB)
downloaded 39 KB

trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/EBImage_4.14.2.zip'
Content type 'application/zip' length 11238868 bytes (10.7 MB)
downloaded 5.3 MB

package ‘BiocGenerics’ successfully unpacked and MD5 sums checked
package ‘abind’ successfully unpacked and MD5 sums checked
Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : 
  cannot open the connection
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 5537792 != reported length 11238868
2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
  cannot open compressed file 'EBImage/DESCRIPTION', probable reason 'No such file or directory'
> library(EBImage)
Error in library(EBImage) : there is no package called ‘EBImage’
> biocLite("EBImage")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.0 (2016-05-03).
Installing package(s) ‘EBImage’
trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/EBImage_4.14.2.zip'
Content type 'application/zip' length 11238868 bytes (10.7 MB)
downloaded 10.7 MB

package ‘EBImage’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Gean\AppData\Local\Temp\RtmpEnNb2N\downloaded_packages
Old packages: 'cluster', 'codetools', 'foreign', 'lattice', 'Matrix', 'mgcv', 'nlme', 'survival'
Update all/some/none? [a/s/n]: 
n
> library(EBImage)
Error in library.dynam(lib, package, package.lib) : 
  DLL ‘tiff’ not found: maybe not installed for this architecture?
Error: package or namespace load failed for ‘EBImage’

ADD REPLYlink written 2.6 years ago by jeankarlosbarrosgalote10
Answer: how install the package EBIamge on the software R 3.3.1?
0
gravatar for Wolfgang Huber
2.6 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:

It's possible that your R installation is corrupt.

To eliminate this possibility can you try with completely removing R, installation it again from CRAN, then running biocLite("EBImage") again (which automatically also gets all the dependencies, incl. abind.)

 

ADD COMMENTlink written 2.6 years ago by Wolfgang Huber13k

this error appears:

 

>library("EBImage", lib.loc="~/R/win-library/3.3")
Error in library.dynam(lib, package, package.lib) : 
  DLL ‘locfit’ not found: maybe not installed for this architecture?
Error: package or namespace load failed for ‘EBImage’
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
> biocLite("EBImage")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.0 (2016-05-03).
Installing package(s) ‘EBImage’
trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/EBImage_4.14.2.zip'
Content type 'application/zip' length 11238868 bytes (10.7 MB)
downloaded 5.1 MB

Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : 
  cannot open the connection
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 5304320 != reported length 11238868
2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
  cannot open compressed file 'EBImage/DESCRIPTION', probable reason 'No such file or directory'

ADD REPLYlink written 2.6 years ago by jeankarlosbarrosgalote10
Answer: how install the package EBIamge on the software R 3.3.1?
0
gravatar for jeankarlosbarrosgalote
2.6 years ago by
jeankarlosbarrosgalote10 wrote:

this error appeas:

 

> library("EBImage", lib.loc="~/R/win-library/3.3")
Error in library.dynam(lib, package, package.lib) : 
  DLL ‘locfit’ not found: maybe not installed for this architecture?
Error: package or namespace load failed for ‘EBImage’
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
> biocLite("EBImage")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.0 (2016-05-03).
Installing package(s) ‘EBImage’
trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/EBImage_4.14.2.zip'
Content type 'application/zip' length 11238868 bytes (10.7 MB)
downloaded 5.1 MB

Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : 
  cannot open the connection
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 5304320 != reported length 11238868
2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
  cannot open compressed file 'EBImage/DESCRIPTION', probable reason 'No such file or directory'

ADD COMMENTlink written 2.6 years ago by jeankarlosbarrosgalote10
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