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hms-dbmi / scde

R package for analyzing single-cell RNA-seq data
http://pklab.med.harvard.edu/scde
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Error in FUN(X[[i]], ...) #48

Open xuesongjing opened 7 years ago

xuesongjing commented 7 years ago

run command line: scde.error.models(counts = cd, groups = sg, n.cores = 1, threshold.segmentation = TRUE, save.crossfit.plots = FALSE, save.model.plots = FALSE, verbose = 1)

error info: Error in FUN(X[[i]], ...) : trying to get slot "logLik" from an object of a basic class ("function") with no slots

thanks!~

sameet commented 6 years ago

I am getting the same error. When I tried to call the calculate.crossfit.models from the commadline, I could not find that function. So I manually imported the function, and now I get the error papply not found. It turns out that papply cannot be installed on R 3.4+.

crmclean commented 6 years ago

I got the same error, and found the solution here:

http://hms-dbmi.github.io/scde/help.html

If you search for "loglik", it will be either the third or fourth thread. The issue has to do with an error with a conflict within later version of the "flexmix" package. I had to install a previous version of flexmix to avoid this.

After I did this, I got another weird error that went away when I installed the latest version of scde package through devtools.

I hope this helps!

pkharchenko commented 6 years ago

Thanks! It would be great to swap out flex mix dependency. If anyone knows of a fast C++ or C poisson regression implementation we could use, that would help. Best, -peter.

On Jul 20, 2017, at 7:20 PM, crmclean notifications@github.com wrote:

I got the same error, and found the solution here:

http://hms-dbmi.github.io/scde/help.html http://hms-dbmi.github.io/scde/help.html If you search for "loglik", it will be either the third or fourth thread. The issue has to do with an error with a conflict within later version of the "flexmix" package. I had to install a previous version of flexmix to avoid this.

After I did this, I got another weird error that went away when I installed the latest version of scde package through devtools.

I hope this helps!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/hms-dbmi/scde/issues/48#issuecomment-316857387, or mute the thread https://github.com/notifications/unsubscribe-auth/ALT78nO199bGBCc-2GJeH8ziFnseaboLks5sP-CxgaJpZM4OE6iR.

jhsiao999 commented 6 years ago

I got the same error with scde and then installed scde_1.99.4 and flexmix_2.3-13. Then I got a different error message which also seems to be related to flexmix:

Error in new("FLXMRglmCf", FLXMRglmC(..., family = family), mu = mu) : 
  could not find function "new"

I then installed the latest scde 2.4.1 on Bioconductor and got the same error message above. I am running jobs on linux x86_64. Any suggestions or ideas that this may be happening?

Thanks!

leezx commented 6 years ago

I used devtools to install the SCDE. And I got the same problem...

hummuscience commented 6 years ago

This error is still present even after following the suggestion with downgrading flexmix

JEFworks commented 6 years ago

For those still experiencing errors with flexmix despite trying the solution from https://github.com/hms-dbmi/scde/issues/40 , can you please share your sessionInfo() ?

littlenapoleon commented 6 years ago

still the same error! `sessionInfo() R version 3.4.2 (2017-09-28) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936
[3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936 [4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_People's Republic of China.936

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

other attached packages: [1] scde_2.2.0 flexmix_2.3-14 lattice_0.20-35

loaded via a namespace (and not attached): [1] Rcpp_0.12.13 edgeR_3.16.5
[3] splines_3.4.2 BiocGenerics_0.20.0
[5] MASS_7.3-47 BiocParallel_1.8.2
[7] rjson_0.2.15 brew_1.0-6
[9] RcppArmadillo_0.8.100.1.0 minqa_1.2.4
[11] distillery_1.0-4 car_2.1-5
[13] tools_3.4.2 Rook_1.1-1
[15] Lmoments_1.2-3 pbkrtest_0.4-7
[17] nnet_7.3-12 parallel_3.4.2
[19] RMTstat_0.3 grid_3.4.2
[21] Biobase_2.34.0 nlme_3.1-131
[23] mgcv_1.8-22 quantreg_5.34
[25] modeltools_0.2-21 MatrixModels_0.4-1
[27] lme4_1.1-14 Matrix_1.2-11
[29] nloptr_1.0.4 RColorBrewer_1.1-2
[31] extRemes_2.0-8 limma_3.30.13
[33] compiler_3.4.2 pcaMethods_1.66.0
[35] stats4_3.4.2 locfit_1.5-9.1
[37] SparseM_1.77 Cairo_1.5-9 `

littlenapoleon commented 6 years ago

Thank you. The problem is solved after the solution from #40!

hummuscience commented 6 years ago

Redid what installation of flexmix and scde and now it works. Thank you!

davetang commented 6 years ago

Hi,

I'm just trying to follow the tutorial (http://hms-dbmi.github.io/scde/diffexp.html) but when I get to the "Fitting error models" step [using the scde.error.models() function], I get an error (despite using flexmix_2.3-13):

library(scde)
data(es.mef.small)
sg <- factor(gsub("(MEF|ESC).*", "\\1", colnames(es.mef.small)), levels = c("ESC", "MEF"))
names(sg) <- colnames(es.mef.small)  
cd <- clean.counts(es.mef.small, min.lib.size=1000, min.reads = 1, min.detected = 1)
o.ifm <- scde.error.models(counts = cd, groups = sg, n.cores = 1, threshold.segmentation = TRUE, save.crossfit.plots = FALSE, save.model.plots = FALSE, verbose = 1)

cross-fitting cells.
number of pairs:  190 
number of pairs:  190 
total number of pairs:  380 
cross-fitting 380 pairs:
building individual error models.
adjusting library size based on 2000 entries
fitting ESC models:
1 : ESC_10
Classification: weighted 
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots
2 : ESC_11
Classification: weighted 
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots
...

I get the same error using my MacBook Pro and the Bioconductor Docker container. Below is my sessionInfo() from running R inside Docker:

sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.19.so

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=C              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] devtools_1.13.4 scde_1.99.1     flexmix_2.3-13  lattice_0.20-35

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.15              compiler_3.4.2            RColorBrewer_1.1-2        nloptr_1.0.4              tools_3.4.2              
 [6] Lmoments_1.2-3            digest_0.6.14             lme4_1.1-15               memoise_1.1.0             nlme_3.1-131             
[11] mgcv_1.8-23               Matrix_1.2-12             curl_3.1                  yaml_2.1.16               parallel_3.4.2           
[16] SparseM_1.77              RcppArmadillo_0.8.300.1.0 httr_1.3.1                withr_2.1.1               knitr_1.18               
[21] extRemes_2.0-8            MatrixModels_0.4-1        locfit_1.5-9.1            stats4_3.4.2              grid_3.4.2               
[26] nnet_7.3-12               Biobase_2.38.0            R6_2.2.2                  distillery_1.0-4          Rook_1.1-1               
[31] BiocParallel_1.12.0       limma_3.34.6              minqa_1.2.4               car_2.1-6                 edgeR_3.20.7             
[36] pcaMethods_1.70.0         modeltools_0.2-21         MASS_7.3-48               BiocGenerics_0.24.0       splines_3.4.2            
[41] RMTstat_0.3               pbkrtest_0.4-7            quantreg_5.34             brew_1.0-6                rjson_0.2.15             
[46] Cairo_1.5-9
JEFworks commented 6 years ago

Hi Dave,

Thanks for the thorough error report. I'm surprised the Docker container is also affected.

Can you please try knn.error.models instead of scde.error.models? If a different error pops up, it'll tell us more about where it originates.

Also, as you are on a Mac, do you have gfortran installed? You can check with gfortran --version

Thanks!

davetang commented 6 years ago

Hi Jean,

thanks for the reply. I tried the example code for knn.error.models but I still got a similar error:

library(scde)
data(pollen)
cd <- clean.counts(pollen)
knn <- knn.error.models(cd, k=ncol(cd)/4, n.cores=1, min.count.threshold=2, min.nonfailed=5, max.model.plots=10)
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots
Error in FUN(X[[i]], ...) : 
  trying to get slot "logLik" from an object of a basic class ("function") with no slots
Error in FUN(X[[i]], ...) : 
...

Here's my sessionInfo():

R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C             
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] 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] devtools_1.13.4 scde_1.99.1     flexmix_2.3-13  lattice_0.20-35

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.15              compiler_3.4.2            RColorBrewer_1.1-2        nloptr_1.0.4             
 [5] tools_3.4.2               Lmoments_1.2-3            digest_0.6.14             lme4_1.1-15              
 [9] memoise_1.1.0             nlme_3.1-131              mgcv_1.8-23               Matrix_1.2-12            
[13] curl_3.1                  yaml_2.1.16               parallel_3.4.2            SparseM_1.77             
[17] RcppArmadillo_0.8.300.1.0 httr_1.3.1                withr_2.1.1               knitr_1.18               
[21] extRemes_2.0-8            MatrixModels_0.4-1        locfit_1.5-9.1            stats4_3.4.2             
[25] grid_3.4.2                nnet_7.3-12               Biobase_2.38.0            R6_2.2.2                 
[29] distillery_1.0-4          Rook_1.1-1                BiocParallel_1.12.0       limma_3.34.6             
[33] minqa_1.2.4               car_2.1-6                 edgeR_3.20.7              pcaMethods_1.70.0        
[37] modeltools_0.2-21         MASS_7.3-48               BiocGenerics_0.24.0       splines_3.4.2            
[41] RMTstat_0.3               pbkrtest_0.4-7            quantreg_5.34             brew_1.0-6               
[45] rjson_0.2.15              Cairo_1.5-9

Regarding gfortran on my Mac, I got:

gfortran --version
gfortran: warning: couldn’t understand kern.osversion ‘17.3.0
GNU Fortran (GCC) 4.8.2
Copyright (C) 2013 Free Software Foundation, Inc.

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING

Here's my Dockerfile:

FROM bioconductor/release_core2

RUN apt-get update
RUN apt-get install -y libcairo2-dev libxt-dev

ADD install_package.R /src/
RUN /src/install_package.R

WORKDIR /work

And install_package.R:

#!/usr/bin/env Rscript

source('https://bioconductor.org/biocLite.R');

biocLite(c(
  'pcaMethods',
  'edgeR'
))

biocLite(ask=FALSE)

install.packages(c(
  'Rook',
  'devtools',
  'Cairo',
  'RMTstat',
  'extRemes',
  'flexmix',
  'RcppArmadillo',
  'rjson',
  'Cairo'
), repos='http://cran.r-project.org')

And I ran RStudio from the Docker container and installed scde and the older version of flexmix prior to running knn.error.models:

download.file(url = "https://github.com/hms-dbmi/scde/archive/1.99.2.tar.gz", destfile = "1.99.2.tar.gz")
install.packages("1.99.2.tar.gz", repos = NULL, type = 'source', dependencies = TRUE)
install.packages("devtools")
library(devtools)
install_version("flexmix", version = "2.3-13", repos = "http://cran.us.r-project.org")

Thanks for your help,

Dave

davetang commented 6 years ago

Hi Jean,

I just used the newest Docker Container and repeated the steps above. I get a different error with knn.error.models:

download.file(url = "https://github.com/hms-dbmi/scde/archive/1.99.2.tar.gz", destfile = "1.99.2.tar.gz")
install.packages("1.99.2.tar.gz", repos = NULL, type = 'source', dependencies = TRUE)
library(devtools)
install_version("flexmix", version = "2.3-13", repos = "http://cran.us.r-project.org")

library(scde)
data(pollen)
cd <- clean.counts(pollen)
knn <- knn.error.models(cd, k=ncol(cd)/4, n.cores=1, min.count.threshold=2, min.nonfailed=5, max.model.plots=10)
Error in checkSlotAssignment(object, name, value) : 
  assignment of an object of class “expression” is not valid for slot ‘defineComponent’ in an object of class “FLXMRglmC”; is(value, "expressionOrfunction") is not TRUE
Error in checkSlotAssignment(object, name, value) : 
  assignment of an object of class “expression” is not valid for slot ‘defineComponent’ in an object of class “FLXMRglmC”; is(value, "expressionOrfunction") is not TRUE
...

Here's my sessionInfo():

R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.19.so

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=C              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] scde_1.99.1     flexmix_2.3-13  lattice_0.20-35 devtools_1.13.4

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.15              nloptr_1.0.4              compiler_3.4.3            RColorBrewer_1.1-2        tools_3.4.3              
 [6] Lmoments_1.2-3            lme4_1.1-15               digest_0.6.14             memoise_1.1.0             nlme_3.1-131             
[11] mgcv_1.8-23               Matrix_1.2-12             curl_3.1                  yaml_2.1.16               parallel_3.4.3           
[16] SparseM_1.77              RcppArmadillo_0.8.300.1.0 withr_2.1.1               httr_1.3.1                extRemes_2.0-8           
[21] MatrixModels_0.4-1        locfit_1.5-9.1            stats4_3.4.3              grid_3.4.3                nnet_7.3-12              
[26] Biobase_2.38.0            R6_2.2.2                  distillery_1.0-4          Rook_1.1-1                BiocParallel_1.12.0      
[31] minqa_1.2.4               limma_3.34.6              car_2.1-6                 edgeR_3.20.7              splines_3.4.3            
[36] pcaMethods_1.70.0         modeltools_0.2-21         MASS_7.3-48               BiocGenerics_0.24.0       pbkrtest_0.4-7           
[41] RMTstat_0.3               brew_1.0-6                quantreg_5.34             rjson_0.2.15              Cairo_1.5-9

Thanks,

Dave

JEFworks commented 6 years ago

Hi Dave, Let me loop in Simon Steigler who made the Docker Container in case he has any advice or has seen this error before.

Simon, do you happen to have seen any of these errors before or have recommendations for troubleshooting? Thanks for any advice!

On Jan 26, 2018, at 7:00 AM, Dave Tang notifications@github.com<mailto:notifications@github.com> wrote:

Hi Jean,

I just used the newest Docker Containerhttps://urldefense.proofpoint.com/v2/url?u=https-3A__hub.docker.com_r_bioconductor_release-5Fcore2_&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=2gb0vmLv11Vi98WTAqlCXyDkhi11d9lKeGWDXEU-qNw&m=XZzUpMcxtb44tZHwWqnbjq1glkpCf5URn2sy0W0g-78&s=vthOcXUH0xQDBFWtSLDYjDov4NXKh07TFA_U1pnPshk&e= and repeated the steps above. I get a different error with knn.error.models:

download.file(url = "https://github.com/hms-dbmi/scde/archive/1.99.2.tar.gz", destfile = "1.99.2.tar.gz") install.packages("1.99.2.tar.gz", repos = NULL, type = 'source', dependencies = TRUE) library(devtools) install_version("flexmix", version = "2.3-13", repos = "http://cran.us.r-project.org")

library(scde) data(pollen) cd <- clean.counts(pollen) knn <- knn.error.models(cd, k=ncol(cd)/4, n.cores=1, min.count.threshold=2, min.nonfailed=5, max.model.plots=10) Error in checkSlotAssignment(object, name, value) : assignment of an object of class “expression” is not valid for slot ‘defineComponent’ in an object of class “FLXMRglmC”; is(value, "expressionOrfunction") is not TRUE Error in checkSlotAssignment(object, name, value) : assignment of an object of class “expression” is not valid for slot ‘defineComponent’ in an object of class “FLXMRglmC”; is(value, "expressionOrfunction") is not TRUE ...

Here's my sessionInfo():

R version 3.4.3 (2017-11-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default BLAS: /usr/lib/openblas-base/libblas.so.3 LAPACK: /usr/lib/libopenblasp-r0.2.19.so

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=C 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] scde_1.99.1 flexmix_2.3-13 lattice_0.20-35 devtools_1.13.4

loaded via a namespace (and not attached): [1] Rcpp_0.12.15 nloptr_1.0.4 compiler_3.4.3 RColorBrewer_1.1-2 tools_3.4.3 [6] Lmoments_1.2-3 lme4_1.1-15 digest_0.6.14 memoise_1.1.0 nlme_3.1-131 [11] mgcv_1.8-23 Matrix_1.2-12 curl_3.1 yaml_2.1.16 parallel_3.4.3 [16] SparseM_1.77 RcppArmadillo_0.8.300.1.0 withr_2.1.1 httr_1.3.1 extRemes_2.0-8 [21] MatrixModels_0.4-1 locfit_1.5-9.1 stats4_3.4.3 grid_3.4.3 nnet_7.3-12 [26] Biobase_2.38.0 R6_2.2.2 distillery_1.0-4 Rook_1.1-1 BiocParallel_1.12.0 [31] minqa_1.2.4 limma_3.34.6 car_2.1-6 edgeR_3.20.7 splines_3.4.3 [36] pcaMethods_1.70.0 modeltools_0.2-21 MASS_7.3-48 BiocGenerics_0.24.0 pbkrtest_0.4-7 [41] RMTstat_0.3 brew_1.0-6 quantreg_5.34 rjson_0.2.15 Cairo_1.5-9

Thanks,

Dave

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_hms-2Ddbmi_scde_issues_48-23issuecomment-2D360767378&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=2gb0vmLv11Vi98WTAqlCXyDkhi11d9lKeGWDXEU-qNw&m=XZzUpMcxtb44tZHwWqnbjq1glkpCf5URn2sy0W0g-78&s=e1hiD9_wOM3-E7KHuDquvoM03H8z4c-9XYMrxVVqwlA&e=, or mute the threadhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AIj2SNeH8m6Scn0JRv6AKvrDkTyEMb1xks5tOb5MgaJpZM4OE6iR&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=2gb0vmLv11Vi98WTAqlCXyDkhi11d9lKeGWDXEU-qNw&m=XZzUpMcxtb44tZHwWqnbjq1glkpCf5URn2sy0W0g-78&s=dqgtMGYU5h1KdfBCdw_J5iFL_0sbv82w2006__sDk9I&e=.

JEFworks commented 6 years ago

Hi Jean, Hi Dave,

I am actually not sure whats going on here. I tried to reproduce your error, but with the docker I had to try out (R-3.4.1). I installed the dependencies and the package scde with biocLite. Afterwards I installed the older version of flexmix. For me knn.error.models worked afterwards. It might have to do with R-3.4.3. I would need to do some testing here, to figure out what the problem is.

Will come back to you, when I get my hands on a R-3.4.3 docker. Maybe you can also try it with an older R and see if the same error is occurring.

Best, Simon

On 29. Jan 2018, at 17:42, Fan, Jean jeanfan@fas.harvard.edu<mailto:jeanfan@fas.harvard.edu> wrote:

Hi Dave, Let me loop in Simon Steigler who made the Docker Container in case he has any advice or has seen this error before.

Simon, do you happen to have seen any of these errors before or have recommendations for troubleshooting? Thanks for any advice!

On Jan 26, 2018, at 7:00 AM, Dave Tang notifications@github.com<mailto:notifications@github.com> wrote:

Hi Jean,

I just used the newest Docker Containerhttps://urldefense.proofpoint.com/v2/url?u=https-3A__hub.docker.com_r_bioconductor_release-5Fcore2_&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=2gb0vmLv11Vi98WTAqlCXyDkhi11d9lKeGWDXEU-qNw&m=XZzUpMcxtb44tZHwWqnbjq1glkpCf5URn2sy0W0g-78&s=vthOcXUH0xQDBFWtSLDYjDov4NXKh07TFA_U1pnPshk&e= and repeated the steps above. I get a different error with knn.error.models:

download.file(url = "https://github.com/hms-dbmi/scde/archive/1.99.2.tar.gz", destfile = "1.99.2.tar.gz") install.packages("1.99.2.tar.gz", repos = NULL, type = 'source', dependencies = TRUE) library(devtools) install_version("flexmix", version = "2.3-13", repos = "http://cran.us.r-project.orghttp://cran.us.r-project.org/")

library(scde) data(pollen) cd <- clean.counts(pollen) knn <- knn.error.models(cd, k=ncol(cd)/4, n.cores=1, min.count.threshold=2, min.nonfailed=5, max.model.plots=10) Error in checkSlotAssignment(object, name, value) : assignment of an object of class “expression” is not valid for slot ‘defineComponent’ in an object of class “FLXMRglmC”; is(value, "expressionOrfunction") is not TRUE Error in checkSlotAssignment(object, name, value) : assignment of an object of class “expression” is not valid for slot ‘defineComponent’ in an object of class “FLXMRglmC”; is(value, "expressionOrfunction") is not TRUE ...

Here's my sessionInfo():

R version 3.4.3 (2017-11-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default BLAS: /usr/lib/openblas-base/libblas.so.3 LAPACK: /usr/lib/libopenblasp-r0.2.19.so

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=C 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] scde_1.99.1 flexmix_2.3-13 lattice_0.20-35 devtools_1.13.4

loaded via a namespace (and not attached): [1] Rcpp_0.12.15 nloptr_1.0.4 compiler_3.4.3 RColorBrewer_1.1-2 tools_3.4.3 [6] Lmoments_1.2-3 lme4_1.1-15 digest_0.6.14 memoise_1.1.0 nlme_3.1-131 [11] mgcv_1.8-23 Matrix_1.2-12 curl_3.1 yaml_2.1.16 parallel_3.4.3 [16] SparseM_1.77 RcppArmadillo_0.8.300.1.0 withr_2.1.1 httr_1.3.1 extRemes_2.0-8 [21] MatrixModels_0.4-1 locfit_1.5-9.1 stats4_3.4.3 grid_3.4.3 nnet_7.3-12 [26] Biobase_2.38.0 R6_2.2.2 distillery_1.0-4 Rook_1.1-1 BiocParallel_1.12.0 [31] minqa_1.2.4 limma_3.34.6 car_2.1-6 edgeR_3.20.7 splines_3.4.3 [36] pcaMethods_1.70.0 modeltools_0.2-21 MASS_7.3-48 BiocGenerics_0.24.0 pbkrtest_0.4-7 [41] RMTstat_0.3 brew_1.0-6 quantreg_5.34 rjson_0.2.15 Cairo_1.5-9

Thanks,

Dave

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sridewi1 commented 4 years ago

Hi Jean,

I am facing the same problem even after using flexmix_2.3-13. 

 knn <- knn.error.models(cd, k = ncol(cd)/3, n.cores = 1, min.count.threshold = 2, min.nonfailed = 5, max.model.plots = 10)
Error in FUN(X[[i]], ...) :
  versuche einen Slot "logLik" von einem Objekt der einfachen Klasse ("function") ohne Slots anzufordern
Error in FUN(X[[i]], ...) :
  versuche einen Slot "logLik" von einem Objekt der einfachen Klasse ("function") ohne Slots anzufordern
Error in FUN(X[[i]], ...) :
  versuche einen Slot "logLik" von einem Objekt der einfachen Klasse ("function") ohne Slots anzufordern
Error in FUN(X[[i]], ...) :
  versuche einen Slot "logLik" von einem Objekt der einfachen Klasse ("function") ohne Slots anzufordern
Error in FUN(X[[i]], ...) :
  versuche einen Slot "logLik" von einem Objekt der einfachen Klasse ("function") ohne Slots anzufordern

here are my sessionInfo()

R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS

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=de_DE.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8
 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C

attached base packages:
 [1] splines   grid      parallel  stats4    stats     graphics  grDevices
 [8] utils     datasets  methods   base

other attached packages:
 [1] devtools_2.2.1              usethis_1.5.1
 [3] dplyr_0.8.3                 gageData_2.22.0
 [5] gage_2.34.0                 pathview_1.24.0
 [7] org.Hs.eg.db_3.8.2          AnnotationDbi_1.46.1
 [9] msigdbr_7.0.1               DOSE_3.10.2
[11] enrichplot_1.4.0            ggrepel_0.8.1
[13] edge_2.16.0                 edgeR_3.26.8
[15] limma_3.40.6                stringr_1.4.0
[17] plyr_1.8.4                  VennDiagram_1.6.20
[19] futile.logger_1.4.3         ReactomePA_1.28.0
[21] clusterProfiler_3.12.0      gplots_3.0.1.1
[23] ggplot2_3.2.1               vsn_3.52.0
[25] data.table_1.12.6           DESeq2_1.24.0
[27] SummarizedExperiment_1.14.1 DelayedArray_0.10.0
[29] BiocParallel_1.18.1         matrixStats_0.55.0
[31] Biobase_2.44.0              GenomicRanges_1.36.1
[33] GenomeInfoDb_1.20.0         IRanges_2.18.3
[35] S4Vectors_0.22.1            BiocGenerics_0.30.0
[37] scde_2.12.0                 flexmix_2.3-13
[39] lattice_0.20-38

Is there any other solutions? thank you in advance for any kind of helps!

Dewi