R error when detecting DAS genes
Closed this issue · 32 comments
Hi, I am following the tutorial using the data as explained.
When I run the DAS code:
$ liqa -task diff -condition_1 list1 -condition_2 list2 -out das_detection_results
I get an error presumably from R:
Error in names(x) <- value :
'names' attribute [2] must be the same length as the vector [0]
Calls: colnames<-
Execution halted
Any ideas how I can get around this? A student is hoping to use LIQA for her honours thesis due next week so your support would be greatly appreciated. Best wishes.
Hi,
Thank you for interests in using LIQA and PennSeq.
Can you upload a sample file in list1 to facilitate my debugging?
Thanks!
Hello. As a technical replicate, I installed LIQA using pip on a second machine (both running MacOS)
Again, using the example data, I can get to the 'diff' step before I am stopped by an error:
$ liqa -task diff -condition_1 list1 -condition_2 list2 -out das_detection_results
Error in names(x) <- value :
'names' attribute [2] must be the same length as the vector [0]
Calls: colnames<-
Execution halted
I have the same question.@huyustats
Thanks!
Hi,
Thank you for interests in using LIQA and PennSeq.
Can you upload a sample file in list1 to facilitate my debugging?
Thanks!
I have the same question
Thank you for your interests in using LIQA. This bug was fixed and please upgriade LIQA to 1.1.18+. Thanks!
Thanks for the answer @huyustats
Could you provide a description of the software results file, for example, how is RelativeAbundance calculated?
Thanks!
Hi @huyustats,
I have encountered ther same error while trying to run liqa -task diff.
Error in names(x) <- value :
'names' attribute [2] must be the same length as the vector [0]
Calls: colnames<-
Execution halted
I also encountered following error while running liqa -task quantify:
Traceback (most recent call last):
File "/usr/local/software/liqa/1.1.18/lib/python3.6/site-packages/liqa_src/quantify.py", line 153, in
for read in bamFilePysam.fetch(geneChr, geneStart, geneEnd):
File "pysam/libcalignmentfile.pyx", line 1082, in pysam.libcalignmentfile.AlignmentFile.fetch
File "pysam/libchtslib.pyx", line 688, in pysam.libchtslib.HTSFile.parse_region
ValueError: invalid coordinates: start (10140462) > stop (9976751)
I have the latest version of LIQA (1.1.18) with required deps installed. The errors occur while I am trying to use my own data. The analysis with provided dummy files works fine. My datafiles were checked multiple times - they are perfectly fine. The formats are ok. They were used for multiple analyses, with various tools and none of them threw an error.
Would you be so kind and provide some sort of solution?
Best regards,
N.
Hi @nemitheasura,
Could you upload the refgene file you used? I will check it. Thanks!
Hi @huyustats,
you will find my refgene attached. I changed an extension to txt in order to be able to upload.
I hope that will help.
Best,
N.
liqa.refgene.txt
I also met the same problem. When I tried to run das using my own data, it stopped by errors.
Error in optim(start, fn.opt, method = method, control = control) :
initial value in 'vmmin' is not finite
Error in chol.default(K) :
the leading minor of order 23 is not positive definite
Error in chol.default(K) :
the leading minor of order 23 is not positive definite
Error in names(x) <- value :
'names' attribute [2] must be the same length as the vector [0]
Calls: colnames<-
Execution halted
Would you be so kind and provide some sort of solution?
Thanks!
I had the same issue.
The error
"Error in chol.default(K) :
the leading minor of order 23 is not positive definite"
is an error in the R package gcmr when a model fails to be constructed for a given gene. It just means that the model cannot be fit. This by itself does not cause an error in LIQA because the model construction is in a try statement, though the error text gets printed.
The script fails however, because models failed to be constructed for every gene. We get the error
'names' attribute [2] must be the same length as the vector [0]
Calls: colnames<-
Execution halted
because the final dataframe reporting the DAS results is empty, and you cannot assign column names to an empty dataframe. Thus it's a one line bug fix, but at any rate the DAS result would be empty anyway.
I already installed gcmr package. Still, I got the same error.
sudo liqa -task diff -condition_1 estimation/control_isoform_exp
ression_estimates -condition_2 estimation/treatment_isoform_expression_estimates -out ./control_treatment_result
[sudo] password for rverma:
Error in library("gcmr") : there is no package called ‘gcmr’
Execution halted
Could you please tell me what is wrong. should I run this command in R? If not, why it shows this error.
Thanks in advance.
I already installed gcmr package. Still, I got the same error.
sudo liqa -task diff -condition_1 estimation/control_isoform_exp ression_estimates -condition_2 estimation/treatment_isoform_expression_estimates -out ./control_treatment_result [sudo] password for rverma: Error in library("gcmr") : there is no package called ‘gcmr’ Execution halted
Could you please tell me what is wrong. should I run this command in R? If not, why it shows this error.
Thanks in advance.
Hi,
it seems that you did not install gcmr successfully. Please make sure gcmr successfully installed by testing library(gcmr) in R.
Thanks
I resolved my last query but now I got a new error. Please give your insight. liqa -task diff -condition_1 list1 -condition_2 list2 -out controlDAStreatment DAS testing: Gene PSMB3 being processed...Error in chol.default(K) : the leading minor of order 13 is not positive definite Error in chol.default(K) : the leading minor of order 13 is not positive definite Error in if (grepl("Error", fit.H0) == T) { : the condition has length > 1 Execution halted Thanks & Regards Rashi (Ph.D.) Post-Doctoral Fellow Neuroscience Institute Morehouse School of Medicine 720 Westview Dr SW, Atlanta, Georgia, USA
…
On Wed, Apr 12, 2023 at 10:02 AM Rashi verma @.> wrote: Thank you for your response. It works without sudo but now it generated another error. liqa -task diff -condition_1 ../estimation/control_isoform_expression_estimates -condition_2 ../estimation/treatment_isoform_expression_estimates -out controlDAStreatment Error in read.table(input.file[1]) : no lines available in input Execution halted I checked my input 1, it is not empty. Kindly give your insight. I will be grateful for your help. Thanks & Regards Rashi (Ph.D.) Post-Doctoral Fellow Neuroscience Institute Morehouse School of Medicine 720 Westview Dr SW, Atlanta, Georgia, USA On Wed, Apr 12, 2023 at 12:20 AM Kai Wang @.> wrote: > when you use sudo to run a software like liqa, the R installation may not > be the same R installation as a user. > > On Tue, Apr 11, 2023 at 11:17 PM rvermamsm @.> wrote: > > > I tested multiple times in R. It installed properly. Still it gives me > the > > same error.Sent from my iPhoneOn 11-Apr-2023, at 6:12 PM, huyustats > > @.> wrote: > > > > I already installed gcmr package. Still, I got the same error. > > sudo liqa -task diff -condition_1 estimation/control_isoform_exp > > ression_estimates -condition_2 > > estimation/treatment_isoform_expression_estimates -out > > ./control_treatment_result [sudo] password for rverma: Error in > > library("gcmr") : there is no package called ‘gcmr’ Execution halted > > Could you please tell me what is wrong. should I run this command in R? > If > > not, why it shows this error. > > Thanks in advance. > > > > Hi, > > it seems that you did not install gcmr successfully. Please make sure > gcmr > > successfully installed by testing library(gcmr) in R. > > Thanks > > > > —Reply to this email directly, view it on GitHub, or unsubscribe.You are > > receiving this because you commented.Message ID: @.> > > > > — > > Reply to this email directly, view it on GitHub > > <#5 (comment)>, or > > unsubscribe > > < > https://github.com/notifications/unsubscribe-auth/ABNG3OFIL763DFOAO3HWM5TXAYNDFANCNFSM45CKUC5Q > > > > . > > You are receiving this because you are subscribed to this thread.Message > > ID: @.> > > > > — > Reply to this email directly, view it on GitHub > <#5 (comment)>, or > unsubscribe > https://github.com/notifications/unsubscribe-auth/A7DUJUON5DFX2ARIWEXKJHDXAYUPZANCNFSM45CKUC5Q > . > You are receiving this because you commented.Message ID: > @.***> >
Hi, the issue maybe still from input file. I will have a test on the code.
Thanks
I also run example data mentioned in a tutorial on github "WGLab/LIQA: Long-read Isoform Quantification and Analysis (github.com) https://github.com/WGLab/LIQA". It has shown the same error : "Error in if (grepl("Error", fit.H0) == T) { : the condition has length > 1 Execution halted" Could you please suggest a solution? Am I doing something wrong? Thanks & Regards Rashi (Ph.D.) Post-Doctoral Fellow Neuroscience Institute Morehouse School of Medicine 720 Westview Dr SW, Atlanta, Georgia, USA
…
On Wed, Apr 12, 2023 at 1:16 PM Rashi verma @.> wrote: Yes, please look into it and let me know as soon as possible. Thanks & Regards Rashi (Ph.D.) Post-Doctoral Fellow Neuroscience Institute Morehouse School of Medicine 720 Westview Dr SW, Atlanta, Georgia, USA On Wed, Apr 12, 2023 at 10:28 AM huyustats @.> wrote: > I resolved my last query but now I got a new error. Please give your > insight. liqa -task diff -condition_1 list1 -condition_2 list2 -out > controlDAStreatment DAS testing: Gene PSMB3 being processed...Error in > chol.default(K) : the leading minor of order 13 is not positive definite > Error in chol.default(K) : the leading minor of order 13 is not positive > definite Error in if (grepl("Error", fit.H0) == T) { : the condition has > length > 1 Execution halted Thanks & Regards Rashi (Ph.D.) Post-Doctoral > Fellow Neuroscience Institute Morehouse School of Medicine 720 Westview Dr > SW, Atlanta, Georgia, USA > … <#m_-7848516770490451371_m_-3011887697266697994_> > On Wed, Apr 12, 2023 at 10:02 AM Rashi verma @.> wrote: Thank you for > your response. It works without sudo but now it generated another error. > liqa -task diff -condition_1 > ../estimation/control_isoform_expression_estimates -condition_2 > ../estimation/treatment_isoform_expression_estimates -out > controlDAStreatment Error in read.table(input.file[1]) : no lines available > in input Execution halted I checked my input 1, it is not empty. Kindly > give your insight. I will be grateful for your help. Thanks & Regards Rashi > (Ph.D.) Post-Doctoral Fellow Neuroscience Institute Morehouse School of > Medicine 720 Westview Dr SW, Atlanta, Georgia, USA On Wed, Apr 12, 2023 at > 12:20 AM Kai Wang @.> wrote: > when you use sudo to run a software like > liqa, the R installation may not > be the same R installation as a user. > > > On Tue, Apr 11, 2023 at 11:17 PM rvermamsm @.> wrote: > > > I > tested multiple times in R. It installed properly. Still it gives me > the > > > same error.Sent from my iPhoneOn 11-Apr-2023, at 6:12 PM, huyustats > > > @.> wrote: > > > > I already installed gcmr package. Still, I got the > same error. > > sudo liqa -task diff -condition_1 > estimation/control_isoform_exp > > ression_estimates -condition_2 > > > estimation/treatment_isoform_expression_estimates -out > > > ./control_treatment_result [sudo] password for rverma: Error in > > > library("gcmr") : there is no package called ‘gcmr’ Execution halted > > > Could you please tell me what is wrong. should I run this command in R? > > If > > not, why it shows this error. > > Thanks in advance. > > > > Hi, > > > it seems that you did not install gcmr successfully. Please make sure > > gcmr > > successfully installed by testing library(gcmr) in R. > > Thanks > > > > > —Reply to this email directly, view it on GitHub, or unsubscribe.You > are > > receiving this because you commented.Message ID: @.> > > > > > — > > Reply to this email directly, view it on GitHub > > <#5 (comment) > <#5 (comment)>>, or > > > unsubscribe > > < > > https://github.com/notifications/unsubscribe-auth/ABNG3OFIL763DFOAO3HWM5TXAYNDFANCNFSM45CKUC5Q > https://github.com/notifications/unsubscribe-auth/ABNG3OFIL763DFOAO3HWM5TXAYNDFANCNFSM45CKUC5Q > > > > > . > > You are receiving this because you are subscribed to this > thread.Message > > ID: @.> > > > > — > Reply to this email directly, > view it on GitHub > <#5 (comment) > <#5 (comment)>>, or > > unsubscribe > > https://github.com/notifications/unsubscribe-auth/A7DUJUON5DFX2ARIWEXKJHDXAYUPZANCNFSM45CKUC5Q > > . > You are receiving this because you commented.Message ID: > @.> > > > > Hi, the issue maybe still from input file. I will have a test on the code. > > Thanks > > — > Reply to this email directly, view it on GitHub > <#5 (comment)>, or > unsubscribe > https://github.com/notifications/unsubscribe-auth/A7DUJUM7NR3LKBCQFAZSVZDXA23YJANCNFSM45CKUC5Q > . > You are receiving this because you commented.Message ID: > @.> >
Hi,
There is no error message on my current PC. I will test it on another server and get back to you.
Thanks,
Yu
Hello WGLab Devlopers, a couple of bumps for this thread,
Issue 1:
Thank you for your response. It works without sudo but now it generated another error. liqa -task diff -condition_1 ../estimation/control_isoform_expression_estimates -condition_2 ../estimation/treatment_isoform_expression_estimates -out controlDAStreatment Error in read.table(input.file[1]) : no lines available in input Execution halted I checked my input 1, it is not empty. Kindly give your insight. I will be grateful for your help. Thanks & Regards Rashi (Ph.D.) Post-Doctoral Fellow Neuroscience Institute Morehouse School of Medicine 720 Westview Dr SW, Atlanta, Georgia, USA
I am currently running into this same error when running LIQA on my own data.
Error in read.table(input.file[1]) : no lines available in input
Execution halted
@rvermamsm How did you solve it?
Issue 2:
I also run example data mentioned in a tutorial on github "WGLab/LIQA: Long-read Isoform Quantification and Analysis (github.com) https://github.com/WGLab/LIQA". It has shown the same error : "Error in if (grepl("Error", fit.H0) == T) { : the condition has length > 1 Execution halted" Could you please suggest a solution? Am I doing something wrong? Thanks & Regards Rashi (Ph.D.) Post-Doctoral Fellow Neuroscience Institute Morehouse School of Medicine 720 Westview Dr SW, Atlanta, Georgia, USA
When running LIQA on the test data, I am also running into a similar error Rashi has been having:
DAS testing: Gene BACE2 being processed...Error in if (grepl("Error", fit.H0) == T) {
:the condition has length > 1
Execution halted
@huyustats Any suggestions as to what may be going on?
Much appreciated,
Raj
Hello WGLab Devlopers, a couple of bumps for this thread,
Issue 1:
Thank you for your response. It works without sudo but now it generated another error. liqa -task diff -condition_1 ../estimation/control_isoform_expression_estimates -condition_2 ../estimation/treatment_isoform_expression_estimates -out controlDAStreatment Error in read.table(input.file[1]) : no lines available in input Execution halted I checked my input 1, it is not empty. Kindly give your insight. I will be grateful for your help. Thanks & Regards Rashi (Ph.D.) Post-Doctoral Fellow Neuroscience Institute Morehouse School of Medicine 720 Westview Dr SW, Atlanta, Georgia, USA
I am currently running into this same error when running LIQA on my own data.
Error in read.table(input.file[1]) : no lines available in input Execution halted@rvermamsm How did you solve it?
Issue 2:
I also run example data mentioned in a tutorial on github "WGLab/LIQA: Long-read Isoform Quantification and Analysis (github.com) https://github.com/WGLab/LIQA". It has shown the same error : "Error in if (grepl("Error", fit.H0) == T) { : the condition has length > 1 Execution halted" Could you please suggest a solution? Am I doing something wrong? Thanks & Regards Rashi (Ph.D.) Post-Doctoral Fellow Neuroscience Institute Morehouse School of Medicine 720 Westview Dr SW, Atlanta, Georgia, USA
When running LIQA on the test data, I am also running into a similar error Rashi has been having:
DAS testing: Gene BACE2 being processed...Error in if (grepl("Error", fit.H0) == T) { :the condition has length > 1 Execution halted@huyustats Any suggestions as to what may be going on?
Much appreciated, Raj
Hi Raj,
Issue 1: My conclusion is the format of input condition file is wrong based on the error message. Can you provide the file you used? I will test the code based on your input.
Issue 2: There is no error when I ran the example data. I will collaborate with our lab members to run this step again to dig out the reason.
Thanks,
Yu
Hello Dr. Hu,
- I believe I solved the first issue. Originally, I had listed the absolute paths of the expression estimate files which were located in a completely different folder. But, then I made an
estimationsubfolder containing the files I needed within the directory where I am trying to the run the script which worked. - But there is still the same "condition has length > 1" error when running the
difftask with my data and the test data.
DAS testing: Gene TMEM229B being processed...Error in while (testhalf & stepFactor < 11) { :
missing value where TRUE/FALSE needed
Error in while (testhalf & stepFactor < 11) { :
missing value where TRUE/FALSE needed
DAS testing: Gene SNRNP200 being processed...Error in if (grepl("Error", fit.H0) == T) { :
the condition has length > 1
Execution halted
Hopefully this can get resolved soon,
Raj
Hi Raj, sorry for the delayed response. I ran this example data, like Dr. Hu did and I did not seem to run into any error. If you are still having problems, you send your input file so I can evaluate what's wrong?
Hello Anagha,
No problem. I do not need to use the diff task for my project so I do not need assistance regarding this anymore.
However, I am not sure if this issue is still prevalent or if it has been fixed in the latest installation of LIQA.
Cheers,
Raj
I have the diff condition has length > 1 error, too
Could you please take a look?
My R is 4.3.1 installed via conda, and python is 3.7.
Thank you
Hi, I believe the program should be able to run with those versions. Try checking issues #32 and #44 and any other related closed issues and those may be able to answer your question!
Thank you for your swift reply. I read them and I'm sure I run it in a x86 docker container. It seems there're conflicts in your installation guide, gcmr 1.0.3 requires R 4.0.0+, and conda forge doesn't have R 3.5.2 but 3.5.3. I guess the error is due to R version. Could you please verify your Python, R, and required dependencies version? Much appreciated!
Hi, my Python version is 3.9.18 and R version is 4.3.1 - gcmr is 1.0.3 for me. Let me know if those versions work on your end!
Hi, my Python version is 3.9.18 and R version is 4.3.1 - gcmr is 1.0.3 for me. Let me know if those versions work on your end!
Hi, thank you for your respose. I installed Python 3.9.18 and R 4.3.1 via anaconda, and installed gcmr 1.0.3 by install install.packages("gcmr"). However, when I followed your tutorial. I still failed at the step 4, liqa -task diff -condition_1 list1 -condition_2 list2 -out das_detection_results, error info is the same,
(liqa) root@63940baa6b4c:/home/download/LIQA_example# liqa -task diff -condition_1 list1 -condition_2 list2 -out das_detection_results
DAS testing: Gene ATP5PF being processed...Error in optim(start, fn.opt, method = method, control = control) :
initial value in 'vmmin' is not finite
Error in if (grepl("Error", fit.H0) == T) { :
the condition has length > 1
Execution halted
My envirnoment is,
(liqa) root@63940baa6b4c:/home/download/LIQA_example# conda list
# packages in environment at /home/software/miniconda3/envs/liqa:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
_r-mutex 1.0.0 anacondar_1
_sysroot_linux-64_curr_repodata_hack 3 haa98f57_10
autograd 1.6.2 pypi_0 pypi
autograd-gamma 0.5.0 pypi_0 pypi
binutils_impl_linux-64 2.38 h2a08ee3_1
binutils_linux-64 2.38.0 hc2dff05_0
blas 1.0 openblas
bwidget 1.9.16 h9eba36c_0
bzip2 1.0.8 h5eee18b_6
c-ares 1.19.1 h5eee18b_0
ca-certificates 2024.7.2 h06a4308_0
cairo 1.16.0 hb05425b_5
contourpy 1.2.1 pypi_0 pypi
curl 8.7.1 hdbd6064_0
cycler 0.12.1 pypi_0 pypi
expat 2.6.2 h6a678d5_0
fontconfig 2.14.1 h4c34cd2_2
fonttools 4.53.1 pypi_0 pypi
formulaic 1.0.2 pypi_0 pypi
freetype 2.12.1 h4a9f257_0
fribidi 1.0.10 h7b6447c_0
future 1.0.0 pypi_0 pypi
gcc_impl_linux-64 11.2.0 h1234567_1
gcc_linux-64 11.2.0 h5c386dc_0
gfortran_impl_linux-64 11.2.0 h1234567_1
gfortran_linux-64 11.2.0 hc2dff05_0
glib 2.78.4 h6a678d5_0
glib-tools 2.78.4 h6a678d5_0
graphite2 1.3.14 h295c915_1
gxx_impl_linux-64 11.2.0 h1234567_1
gxx_linux-64 11.2.0 hc2dff05_0
harfbuzz 4.3.0 hf52aaf7_2
icu 73.1 h6a678d5_0
importlib-resources 6.4.0 pypi_0 pypi
interface-meta 1.3.0 pypi_0 pypi
jpeg 9e h5eee18b_2
kernel-headers_linux-64 3.10.0 h57e8cba_10
kiwisolver 1.4.5 pypi_0 pypi
krb5 1.20.1 h143b758_1
ld_impl_linux-64 2.38 h1181459_1
lerc 3.0 h295c915_0
libcurl 8.7.1 h251f7ec_0
libdeflate 1.17 h5eee18b_1
libedit 3.1.20230828 h5eee18b_0
libev 4.33 h7f8727e_1
libffi 3.4.4 h6a678d5_1
libgcc-devel_linux-64 11.2.0 h1234567_1
libgcc-ng 11.2.0 h1234567_1
libgfortran-ng 11.2.0 h00389a5_1
libgfortran5 11.2.0 h1234567_1
libglib 2.78.4 hdc74915_0
libgomp 11.2.0 h1234567_1
libiconv 1.16 h5eee18b_3
libnghttp2 1.57.0 h2d74bed_0
libopenblas 0.3.21 h043d6bf_0
libpng 1.6.39 h5eee18b_0
libssh2 1.11.0 h251f7ec_0
libstdcxx-devel_linux-64 11.2.0 h1234567_1
libstdcxx-ng 11.2.0 h1234567_1
libtiff 4.5.1 h6a678d5_0
libuuid 1.41.5 h5eee18b_0
libwebp-base 1.3.2 h5eee18b_0
libxcb 1.15 h7f8727e_0
libxml2 2.10.4 hfdd30dd_2
lifelines 0.29.0 pypi_0 pypi
liqa 1.3.0 pypi_0 pypi
lz4-c 1.9.4 h6a678d5_1
make 4.2.1 h1bed415_1
matplotlib 3.9.1 pypi_0 pypi
ncurses 6.4 h6a678d5_0
numpy 1.26.4 pypi_0 pypi
openssl 3.0.14 h5eee18b_0
packaging 24.1 pypi_0 pypi
pandas 2.2.2 pypi_0 pypi
pango 1.50.7 h05da053_0
pcre2 10.42 hebb0a14_1
pillow 10.4.0 pypi_0 pypi
pip 24.0 py39h06a4308_0
pixman 0.40.0 h7f8727e_1
pyparsing 3.1.2 pypi_0 pypi
pysam 0.22.1 pypi_0 pypi
python 3.9.18 h955ad1f_0
python-dateutil 2.9.0.post0 pypi_0 pypi
pytz 2024.1 pypi_0 pypi
r-backports 1.4.1 r43h76d94ec_0
r-base 4.3.1 h1ae530e_0
r-boot 1.3_28.1 r43h6115d3f_0
r-brio 1.1.3 r43h76d94ec_0
r-broom 1.0.5 r43h6115d3f_0
r-callr 3.7.3 r43h6115d3f_0
r-cli 3.6.1 r43h884c59f_0
r-colorspace 2.1_0 r43h76d94ec_0
r-cowplot 1.1.3 r43hc72bb7e_1 conda-forge
r-cpp11 0.4.6 r43h6115d3f_0
r-crayon 1.5.2 r43h6115d3f_0
r-deriv 4.1.3 r43h142f84f_0
r-desc 1.4.2 r43h6115d3f_0
r-diffobj 0.3.5 r43h76d94ec_0
r-digest 0.6.33 r43h884c59f_0
r-doby 4.6.22 r43hc72bb7e_0 conda-forge
r-dplyr 1.1.3 r43h884c59f_0
r-ellipsis 0.3.2 r43h76d94ec_0
r-evaluate 0.22 r43h6115d3f_0
r-fansi 1.0.5 r43h76d94ec_0
r-farver 2.1.1 r43h884c59f_0
r-fs 1.6.3 r43h884c59f_0
r-generics 0.1.3 r43h142f84f_0
r-ggplot2 3.5.1 r43hc72bb7e_1 conda-forge
r-glue 1.6.2 r43h76d94ec_0
r-gtable 0.3.4 r43h6115d3f_0
r-isoband 0.2.7 r43h884c59f_0
r-jsonlite 1.8.7 r43h76d94ec_0
r-labeling 0.4.3 r43h6115d3f_0
r-lattice 0.22_5 r43h76d94ec_0
r-lifecycle 1.0.3 r43h142f84f_0
r-lme4 1.1_34 r43h884c59f_0
r-magrittr 2.0.3 r43h76d94ec_0
r-mass 7.3_60 r43h76d94ec_0
r-matrix 1.6_1.1 r43h76d94ec_0
r-mgcv 1.9_0 r43h76d94ec_0
r-microbenchmark 1.4.10 r43h76d94ec_0
r-minqa 1.2.6 r43hb5eb8f6_0
r-modelr 0.1.11 r43h6115d3f_0
r-munsell 0.5.0 r43h6115d3f_0
r-nlme 3.1_163 r43h640688f_0
r-nloptr 2.0.3 r43hb5eb8f6_0
r-numderiv 2016.8_1.1 r43h6115d3f_0
r-pbkrtest 0.5.2 r43h6115d3f_0
r-pillar 1.9.0 r43h6115d3f_0
r-pkgbuild 1.4.2 r43h142f84f_0
r-pkgconfig 2.0.3 r43h6115d3f_0
r-pkgload 1.3.3 r43h142f84f_0
r-praise 1.0.0 r43h6115d3f_4
r-prettyunits 1.2.0 r43h142f84f_0
r-processx 3.8.2 r43h76d94ec_0
r-ps 1.7.5 r43h76d94ec_0
r-purrr 1.0.2 r43h76d94ec_0
r-r6 2.5.1 r43h6115d3f_0
r-rcolorbrewer 1.1_3 r43h6115d3f_1
r-rcpp 1.0.11 r43h884c59f_0
r-rcppeigen 0.3.3.9.3 r43h884c59f_0
r-rematch2 2.1.2 r43h142f84f_0
r-rlang 1.1.1 r43h884c59f_0
r-rprojroot 2.0.3 r43h6115d3f_0
r-scales 1.2.1 r43h6115d3f_0
r-stringi 1.7.12 r43h884c59f_0
r-stringr 1.5.0 r43h6115d3f_0
r-testthat 3.2.0 r43h884c59f_0
r-tibble 3.2.1 r43h76d94ec_0
r-tidyr 1.3.0 r43h884c59f_0
r-tidyselect 1.2.0 r43h6115d3f_0
r-utf8 1.2.4 r43h76d94ec_0
r-vctrs 0.6.4 r43h884c59f_0
r-viridislite 0.4.2 r43h6115d3f_0
r-waldo 0.5.1 r43h6115d3f_0
r-withr 2.5.1 r43h6115d3f_0
readline 8.2 h5eee18b_0
scipy 1.13.1 pypi_0 pypi
setuptools 69.5.1 py39h06a4308_0
six 1.16.0 pypi_0 pypi
sqlite 3.45.3 h5eee18b_0
sysroot_linux-64 2.17 h57e8cba_10
tk 8.6.14 h39e8969_0
tktable 2.10 h3d55465_1
typing-extensions 4.12.2 pypi_0 pypi
tzdata 2024.1 pypi_0 pypi
wheel 0.43.0 py39h06a4308_0
wrapt 1.16.0 pypi_0 pypi
xz 5.4.6 h5eee18b_1
zipp 3.19.2 pypi_0 pypi
zlib 1.2.13 h5eee18b_1
zstd 1.5.5 hc292b87_2
My command to create the envirnoment and install the packages including LIQA is,
mamba create -n liqa python=3.9.18 r-base=4.3.1
mamba activate liqa
cd LIQA/
pip install .
mamba install conda-forge::r-ggplot2
mamba install conda-forge::r-cowplot
mamba install conda-forge::r-doBy
(in R, install.packages("gcmr"))
Would you please check it? Thanks a lot for your support!