Match name error about fastqcr HOT 14 CLOSED

Hey! Install it from Anaconda bioconda first and don't update packages later. Make a separate environment. It works that way.

from fastqcr.

I’m far from the computer. I will be able to check that next week.

Please, provide the complete output of devtools:session_infos()

from fastqcr.

Thanks for the fast reply, no problem.

Session info -------------------------------------------------------------------------------------------------------------------
setting value
version R version 3.5.0 (2018-04-23)
system x86_64, linux-gnu
ui RStudio (1.1.419)
language (EN)
collate en_US.UTF-8
tz Asia/Tokyo
date 2018-08-23

Packages -----------------------------------------------------------------------------------------------------------------------
package * version date source
assertthat 0.2.0 2017-04-11 CRAN (R 3.5.0)
backports 1.1.2 2017-12-13 CRAN (R 3.5.0)
base * 3.5.0 2018-05-14 local
bindr 0.1.1 2018-03-13 CRAN (R 3.5.0)
bindrcpp * 0.2.2 2018-03-29 CRAN (R 3.5.0)
broom 0.4.5.9000 2018-07-11 Github (tidymodels/broom@05a4889)
cellranger 1.1.0 2016-07-27 CRAN (R 3.5.0)
cli 1.0.0 2017-11-05 CRAN (R 3.5.0)
colorspace 1.3-2 2016-12-14 CRAN (R 3.5.0)
compiler 3.5.0 2018-05-14 local
crayon 1.3.4 2017-09-16 CRAN (R 3.5.0)
datasets * 3.5.0 2018-05-14 local
devtools 1.13.5 2018-02-18 CRAN (R 3.5.0)
digest 0.6.15 2018-01-28 CRAN (R 3.5.0)
dplyr * 0.7.5 2018-05-19 CRAN (R 3.5.0)
evaluate 0.10.1 2017-06-24 CRAN (R 3.5.0)
fastqcr * 0.1.0 2017-04-11 CRAN (R 3.5.0)
forcats * 0.3.0 2018-02-19 CRAN (R 3.5.0)
ggplot2 * 3.0.0 2018-07-03 CRAN (R 3.5.0)
glue 1.3.0 2018-07-17 CRAN (R 3.5.0)
graphics * 3.5.0 2018-05-14 local
grDevices * 3.5.0 2018-05-14 local
grid 3.5.0 2018-05-14 local
gtable 0.2.0 2016-02-26 CRAN (R 3.5.0)
haven 1.1.1 2018-01-18 CRAN (R 3.5.0)
hms 0.4.2.9001 2018-08-22 Github (tidyverse/hms@979286f)
httr 1.3.1 2017-08-20 CRAN (R 3.5.0)
jsonlite 1.5 2017-06-01 CRAN (R 3.5.0)
knitr 1.20 2018-02-20 CRAN (R 3.5.0)
lattice 0.20-35 2017-03-25 CRAN (R 3.5.0)
lazyeval 0.2.1 2017-10-29 CRAN (R 3.5.0)
lubridate 1.7.4 2018-04-11 CRAN (R 3.5.0)
magrittr 1.5 2014-11-22 CRAN (R 3.5.0)
memoise 1.1.0 2017-04-21 CRAN (R 3.5.0)
methods * 3.5.0 2018-05-14 local
modelr 0.1.2.9000 2018-06-21 Github (tidyverse/modelr@28c55db)
munsell 0.5.0 2018-06-12 CRAN (R 3.5.0)
nlme 3.1-137 2018-04-07 CRAN (R 3.5.0)
pillar 1.3.0 2018-07-14 CRAN (R 3.5.0)
pkgconfig 2.0.2 2018-08-16 cran (@2.0.2)
plyr 1.8.4 2016-06-08 CRAN (R 3.5.0)
purrr * 0.2.5 2018-05-29 CRAN (R 3.5.0)
R6 2.2.2 2017-06-17 CRAN (R 3.5.0)
Rcpp 0.12.17 2018-05-18 CRAN (R 3.5.0)
readr * 1.2.0 2018-06-21 Github (tidyverse/readr@05890c3)
readxl 1.1.0 2018-04-20 CRAN (R 3.5.0)
reshape2 1.4.3 2017-12-11 cran (@1.4.3)
rlang 0.2.2 2018-08-16 cran (@0.2.2)
rstudioapi 0.7 2017-09-07 CRAN (R 3.5.0)
rvest 0.3.2 2016-06-17 CRAN (R 3.5.0)
scales 0.5.0.9000 2018-06-21 Github (r-lib/scales@80fe94c)
stats * 3.5.0 2018-05-14 local
stringi 1.2.3 2018-06-12 CRAN (R 3.5.0)
stringr * 1.3.1 2018-05-10 CRAN (R 3.5.0)
tibble * 1.4.2 2018-01-22 CRAN (R 3.5.0)
tidyr * 0.8.1 2018-05-18 CRAN (R 3.5.0)
tidyselect 0.2.4 2018-02-26 CRAN (R 3.5.0)
tidyverse * 1.2.1 2017-11-14 CRAN (R 3.5.0)
tools 3.5.0 2018-05-14 local
utils * 3.5.0 2018-05-14 local
withr 2.1.2 2018-03-15 CRAN (R 3.5.0)
xml2 1.2.0 2018-01-24 CRAN (R 3.5.0)
yaml 2.1.19 2018-05-01 CRAN (R 3.5.0)

from fastqcr.

Any news? It dosn't work for me in any version of R (3.3-3.5).

from fastqcr.

Same here…

from fastqcr.

I have this same error on a fresh install of Ubuntu Bionic Beaver, a fresh install of R, devtools and fastqcr. I'd rather avoid installing and using Bioconda etc. Is there another way to fix the issue?

Also, I'm wondering if the issue is in this line of the code

qc <- qc_read(qc.files[i], modules = c("summary", "statistics", "Sequence Duplication Levels"),
verbose = FALSE)

since when I look at one of my fastqc_data.txt files, the only module out of that list I can find is "Sequence Duplication Levels". So perhaps this is an issue with using an updated version of fastqc? If that's the case, can you clarify which version of fastqc you were using when the code was written because maybe it makes sense to use an older version of fastqc for now?

from fastqcr.

It's not the fault of fastqc but R packages around it.
My working combo after loading fastqcr is :
loaded via a namespace (and not attached):
[1] Rcpp_0.12.18 crayon_1.3.4 dplyr_0.7.6 assertthat_0.2.0
[5] plyr_1.8.4 grid_3.5.1 R6_2.2.2 gtable_0.2.0
[9] magrittr_1.5 scales_0.5.0 ggplot2_3.0.0 pillar_1.3.0
[13] rlang_0.2.1 lazyeval_0.2.1 bindrcpp_0.2.2 glue_1.3.0
[17] munsell_0.5.0 purrr_0.2.5 compiler_3.5.1 colorspace_1.3-2
[21] pkgconfig_2.0.1 bindr_0.1.1 tidyselect_0.2.4 tibble_1.4.2

Someone needs to look into the source code as the author is apparently absent.

from fastqcr.

Thanks for the reply osowiecki, I appreciate it. So I went through and installed all the same versions of the dependencies that you sent to me. There were 2 I couldn't change, grid and compiler. And sure enough, when I tried to run fastqcr again, I still get the same error. Can you confirm osowiecki which version of R you are running? compiler is built in to the R version I'm using so I don't think I can change it. Grid is also not available for my version of R.

from fastqcr.

Thanks for the reply osowiecki, I appreciate it. So I went through and installed all the same versions of the dependencies that you sent to me. There were 2 I couldn't change, grid and compiler. And sure enough, when I tried to run fastqcr again, I still get the same error. Can you confirm osowiecki which version of R you are running? compiler is built in to the R version I'm using so I don't think I can change it. Grid is also not available for my version of R.

R version 3.5.1 (2018-07-02) -- "Feather Spray"

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

other attached packages:
[1] fastqcr_0.1.0

Install fastqcr via conda in a virtual environment. Activate this R environment for fastqcr and use it. Here is more info on how to do it.

http://docs.anaconda.com/anaconda/user-guide/tasks/use-r-language/
https://stackoverflow.com/questions/24283171/virtual-environment-in-r

from fastqcr.

Installing the latest developmental version should now fix this issue.

devtools::install_github("kassambara/fastqcr")

Please , let me know, thanks!

from fastqcr.

devtools::install_github("kassambara/fastqcr")

17 parsing failures.
row # A tibble: 5 x 5 col row col expected actual file expected actual 1 1 NA 2 columns 3 columns literal data file 2 2 NA 2 columns 3 columns literal data row 3 3 NA 2 columns 3 columns literal data col 4 4 NA 2 columns 3 columns literal data expected 5 5 NA 2 columns 3 columns literal data
... ................................. ... .............................................. ........ ........................................................................................................................................................................... ...... ...................................... [... truncated]
in command '.f(.x[[i]], ...)':object not found 'module'

43: In rbind(names(probs), probs_f) :
number of columns of result is not a multiple of vector length (arg 1)

from fastqcr.

OK. Updating all packages seems to fix the issue with new version of fastqcr

sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS/LAPACK: /home/debian/miniconda3/lib/R/lib/libRblas.so

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

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

other attached packages:
[1] bindrcpp_0.2.2 fastqcr_0.1.1

loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 bindr_0.1.1 magrittr_1.5 hms_0.4.2
[5] tidyselect_0.2.5 munsell_0.5.0 colorspace_1.3-2 R6_2.3.0
[9] rlang_0.3.0.1 fansi_0.4.0 plyr_1.8.4 dplyr_0.7.8
[13] grid_3.5.1 gtable_0.2.0 utf8_1.1.4 cli_1.0.0
[17] lazyeval_0.2.1 assertthat_0.2.0 tibble_1.4.2 crayon_1.3.4
[21] purrr_0.2.5 readr_1.2.1 ggplot2_3.1.0 glue_1.3.0
[25] compiler_3.5.1 pillar_1.3.0 scales_1.0.0 pkgconfig_2.0.2

from fastqcr.

so we can close this issue, thanks

from fastqcr.

Hello,

I had the same issue and based on your suggestion, we updated to the newer version (0.1.1) and that error is gone and I was able to generate the qc metrics but some of the modules are NA while it worked with previous version (0.1.0) with same data! Do you have any thoughts?
Thank you.
qc$tot.seq
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[47] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[93] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
qcstat<- qc_stats(qc)

qcstat
sample pct.dup pct.gc tot.seq seq.length

1 C_rep1_R1 72.4 NA NA NA
2 C_rep1_R2 72.8 NA NA NA
3 C_rep2_R1 72.8 NA NA NA
4 C_rep2_R2 72.8 NA NA NA
5 C_rep3_R1 71.6 NA NA NA
6 C_rep3_R2 70.8 NA NA NA
7 P_rep1_R1 69.1 NA NA NA
8 P_rep1_R2 67.9 NA NA NA
9 P_rep2_R1 68.6 NA NA NA
10 P_rep2_R2 67.4 NA NA NA
11 P_rep3_R1 72.3 NA NA NA
12 P_rep3_R2 71.3 NA NA NA

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