Installing lavann - probably a linux problem

[Josef Lauri]

I was working well with lavaan under R version 2.15. When I upgraded to version 3.0.1 (Good Sport) I had to upgrade the lavaan package. This is what I got when I tried 

install.pckages("lavaan")

Installing package into ‘/home/josef/R/x86_64-pc-linux-gnu-library/3.0’

(as ‘lib’ is unspecified)

--- Please select a CRAN mirror for use in this session ---

trying URL 'http://www.freestatistics.org/cran/src/contrib/lavaan_0.5-14.tar.gz'

Content type 'application/x-gzip' length 272379 bytes (265 Kb)

opened URL

==================================================

downloaded 265 Kb

* installing *source* package ‘lavaan’ ...

** package ‘lavaan’ successfully unpacked and MD5 sums checked

** R

** data

*** moving datasets to lazyload DB

** inst

** preparing package for lazy loading

Error : package ‘quadprog’ was built before R 3.0.0: please re-install it

ERROR: lazy loading failed for package ‘lavaan’

* removing ‘/home/josef/R/x86_64-pc-linux-gnu-library/3.0/lavaan’

The downloaded source packages are in

‘/tmp/RtmpcHaMqE/downloaded_packages’

Warning message:

In install.packages("lavaan") :

  installation of package ‘lavaan’ had non-zero exit status

> 

So I tried re-installing quadprog, and I got this.

> install.packages("quadprog")

Installing package into ‘/home/josef/R/x86_64-pc-linux-gnu-library/3.0’

(as ‘lib’ is unspecified)

trying URL 'http://www.freestatistics.org/cran/src/contrib/quadprog_1.5-5.tar.gz'

Content type 'application/x-gzip' length 33651 bytes (32 Kb)

opened URL

==================================================

downloaded 32 Kb

* installing *source* package ‘quadprog’ ...

** package ‘quadprog’ successfully unpacked and MD5 sums checked

** libs

gfortran  -fvisibility=hidden -fpic  -O3 -pipe  -g  -c aind.f -o aind.o

gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c init.c -o init.o

gfortran -fvisibility=hidden -fpic -O3 -pipe  -g -ffloat-store   -c -o solve.QP.compact.o solve.QP.compact.f

gfortran -fvisibility=hidden -fpic -O3 -pipe  -g -ffloat-store   -c -o solve.QP.o solve.QP.f

gfortran  -fvisibility=hidden -fpic  -O3 -pipe  -g  -c util.f -o util.o

gcc -std=gnu99 -shared -o quadprog.so aind.o init.o solve.QP.compact.o solve.QP.o util.o -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR

/usr/bin/ld: cannot find -lblas

collect2: ld returned 1 exit status

make: *** [quadprog.so] Error 1

ERROR: compilation failed for package ‘quadprog’

* removing ‘/home/josef/R/x86_64-pc-linux-gnu-library/3.0/quadprog’

The downloaded source packages are in

‘/tmp/RtmpcHaMqE/downloaded_packages’

Warning message:

In install.packages("quadprog") :

  installation of package ‘quadprog’ had non-zero exit status

> 

This is why I think it might be a problem with the linux installation (I use ubuntu LTS 12.04), because of the "cannot find -lblas" error. Seems like a compilation error.

I also tried the install command with dependencies=TRUE, and I got a much longer response. Basically R downloaded all the packages, but failed to compile successfully any of them. For some it reported that some package was created before version 3.0.0 (as above for quadprog) for most it gave an error while compiling, like

/usr/bin/ld: cannot find -llapack

/usr/bin/ld: cannot find -lblas

I would be grateful for any suggestions.

Thanks.

Josef

[Josef Lauri]

I am getting the same sort of errors if I try to install other packages:

/usr/bin/ld: cannot find -llapack

/usr/bin/ld: cannot find -lblas

So it seems like a g++ problem. But I do not know enough linux to be able to fix this.

Josef

[Josef Lauri]

Found the problem. I had to install r-base-dev. I never had to do that with older versions of R. Probably I used the R which came with the ubuntu I was using, and it was automatically installed. Also, whenever I try to install.packages like "qgraph" the compilation stops several times because of dependencies on other packages which were "installed before Vers 3.0.0" and I had to install these (sometimes these depended on other pre-3.0.0 packages, so I had to drill down deeper). There is surely a more efficient way of doing this but I do not mind as long as I am installing them. And I did not have to do this with versions older than 3.0.0.

So I hope this post could be helpful to R >=3.0.0 users who are not that savvy with linux.

Josef

On Sunday, 18 August 2013 07:58:07 UTC+2, Josef Lauri wrote:

[William Murrah]

When you installed R 3.0, did you re-install all R packages? If not, I wonder if this is related to your problems. See this link for an easy way to do it.

http://www.r-bloggers.com/automated-re-install-of-packages-for-r-3-0/

[Josef Lauri]

Yes, it definitely seems to be related because it indicates possibly a new need for installing new packages in R 3.0.0. Thanks for the link! It seems that the basic packages have been re-installed. But at least if not I know what I have to do.

Josef

[Imran Ramzan]

i facing the same issue while installing the Lavaan, can you please help me that how i can fix it. Thank...

install.packages("C:/Users/Imran/Downloads/lavaan_0.6-3.zip", repos = NULL, type = "win.binary")
Installing package into ‘C:/Users/Imran/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)

package ‘lavaan’ successfully unpacked and MD5 sums checked

[Christopher David Desjardins]

Hi Imran,
What is the error message? What happens when you run:

library(lavaan)

What’s the output from the following

R.version

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[Imran Ramzan]

Hi Christopher, thanks for feedback. I am using Window7 to analyse CFA. For that, i have to install the lavaan package in rstudio.

When i open the rstudio and give the following command:

install.packages("lavaan")

It gives following message:

install.packages("lavaan")

Installing package into ‘C:/Users/Imran/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/lavaan_0.6-3.zip'
Content type 'application/zip' length 2640771 bytes (2.5 MB)
downloaded 2.5 MB

package ‘lavaan’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\Imran\AppData\Local\Temp\Rtmp02mdp6\downloaded_packages

And when i run the command of

library(lavaan)

it reports following message:

> library(lavaan)
Error: package or namespace load failed for ‘lavaan’ in runHook(".onLoad", env, package.lib, package):
 lazy-load database 'C:/Users/Imran/Documents/R/win-library/3.5/mnormt/R/mnormt.rdb' is corrupt
In addition: Warning message:
In runHook(".onLoad", env, package.lib, package) :
  internal error -3 in R_decompress1

[Christopher David Desjardins]

Hi Imran,

Can you do the following,

1. Close RStudio.

2. Open RStudio.

3. Run `install.packages("lavaan")` make sure lavaan isn't loaded before you do this.

4. Try and load lavaan: `library(lavaan)`

Do you still get the same error message?

[Imran Ramzan]

Yes Christopher, issue still persist. :( Could you please assist me as i have to run CFA. please...

[Christopher D Desjardins]

What is your version or R? Can you load any packages that you've installed? For example, does

install.packages("car")

library(car)

Work? If this fails, this seems like a Windows problem. Also, note that lavaan requires a newer version of R (R >= 3.4). So, if you have an old version of R that could be the problem, too.

Chris

[Imran Ramzan]

I am using the latest R version.. Version 1.1.463 – © 2009-2018 RStudio, Inc.  and R3.5.2 

I guess, there is issue in installing other packages as well :(

[Christopher David Desjardins]

Hi Imran,

Unless someone else can help you on here, I would suggest asking this on the R-help mailing list. I'm guessing the issue is because of Windows. I am sure someone can figure it out for you though.

Chris

[koenig...@gmail.com]

Hi Imran,

can you delete (and reinstall) the 'mnormt' package?

Your original error message refers to this package.

If all else fails, try a fresh installation of R and RStudio.

Fingers crossed!

Chris