Comments (17)
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+.
from scde.
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!
from scde.
from scde.
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!
from scde.
I used devtools to install the SCDE. And I got the same problem...
from scde.
This error is still present even after following the suggestion with downgrading flexmix
from scde.
For those still experiencing errors with flexmix despite trying the solution from #40 , can you please share your sessionInfo()
?
from scde.
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 `
from scde.
Thank you. The problem is solved after the solution from #40!
from scde.
Redid what installation of flexmix and scde and now it works. Thank you!
from scde.
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
from scde.
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!
from scde.
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
from scde.
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
from scde.
from scde.
from scde.
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
from scde.
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from scde.