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oloBion / Retip

Retip - Retention Time prediction for metabolomics
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memory not mapped #13

Open Cao-lab-zcmu opened 2 years ago

Cao-lab-zcmu commented 2 years ago

while use function: getCD(HILIC) caused error address 0x7ffeda268fd8, cause 'memory not mapped'

R version is 4.1.0

tobigithub commented 2 years ago

Hi, check that you can load all individual modules? See here for step-by-step process: [Retip Fresh Install] Maybe the RDKIT part can not be loaded?

image T.

Cao-lab-zcmu commented 2 years ago

Hi, check that you can load all individual modules? See here for step-by-step process: [Retip Fresh Install] Maybe the RDKIT part can not be loaded?

image T.

Thanks for your reply. However, I think package 'rcdk' is ok. It can be loaded successfully. The following is the error report.

 *** caught segfault ***
address 0x7ffc82684fb8, cause 'memory not mapped'

Traceback:
 1: .jcall(desc, "Lorg/openscience/cdk/qsar/DescriptorValue;", "calculate",     a, check = check)
 2: tryCatchList(expr, classes, parentenv, handlers)
 3: tryCatch({    .jcall(desc, "Lorg/openscience/cdk/qsar/DescriptorValue;",         "calculate", a, check = check)})
 4: FUN(X[[i]], ...)
 5: lapply(molecules, function(a, check) {    val <- tryCatch({        .jcall(desc, "Lorg/openscience/cdk/qsar/DescriptorValue;",             "calculate", a, check = check)    })}, check = FALSE)
 6: rcdk::eval.desc(mols_x1, descNames)
 7: getCD(HILIC)
Cao-lab-zcmu commented 2 years ago

I checked the Retip codes, and found while excute function:

  descs_x_loop <- rcdk::eval.desc(mols_x1, descNames)

error caused.

tobigithub commented 2 years ago

https://www.rdocumentation.org/packages/rcdk/versions/3.4.7.1/topics/eval.desc

Cao-lab-zcmu commented 2 years ago

Many thanks! While I use example codes given by rcdk::eval.desc, it run successfully.

> smiles <- c('CCC', 'c1ccccc1', 'CC(=O)C')
> mols <- sapply(smiles, parse.smiles)
> 
> dnames <- get.desc.names('constitutional')
> descs <- eval.desc(mols, dnames, verbose=TRUE)
Processing  FractionalCSP3Descriptor 
Processing  XLogPDescriptor 
Processing  WeightDescriptor 
Processing  RuleOfFiveDescriptor 
Processing  RotatableBondsCountDescriptor 
Processing  MannholdLogPDescriptor 
Processing  LongestAliphaticChainDescriptor 
Processing  LargestPiSystemDescriptor 
Processing  LargestChainDescriptor 
Processing  BondCountDescriptor 
Processing  BasicGroupCountDescriptor 
Processing  AtomCountDescriptor 
Processing  AromaticBondsCountDescriptor 
Processing  AromaticAtomsCountDescriptor 
Processing  ALOGPDescriptor 
Processing  AcidicGroupCountDescriptor

However, when I do this with getCD(HILIC), it did failed.

[1] "Computing Chemical Descriptors 1 of 970 ... Please wait"

 *** caught segfault ***
address 0x7ffda9d71fa8, cause 'memory not mapped'

Traceback:
 1: .jcall(desc, "Lorg/openscience/cdk/qsar/DescriptorValue;", "calculate",     a, check = check)
 2: tryCatchList(expr, classes, parentenv, handlers)
 3: tryCatch({    .jcall(desc, "Lorg/openscience/cdk/qsar/DescriptorValue;",         "calculate", a, check = check)})
 4: FUN(X[[i]], ...)
 5: lapply(molecules, function(a, check) {    val <- tryCatch({        .jcall(desc, "Lorg/openscience/cdk/qsar/DescriptorValue;",             "calculate", a, check = check)    })}, check = FALSE)
 6: rcdk::eval.desc(mols_x1, descNames)
 7: getCD(HILIC)
tobigithub commented 2 years ago

Can you send the input data? Tnx

Cao-lab-zcmu commented 2 years ago

Oh, herein I just use the HILIC data. No other dataset was utilized.

> HILIC
# A tibble: 970 × 4
   NAME                                         INCHKEY             SMILES    RT
   <chr>                                        <chr>               <chr>  <dbl>
 1 (2-oxo-2,3-dihydro-1H-indol-3-yl)acetic acid ILGMGHZPXRDCCS-UHF… C1=CC…  2.02
 2 1,1-Dimethyl-4-phenylpiperazinium            WVHNHHJEHFWYHH-UHF… CC1C(…  2.61
 3 1,2-Cyclohexanediol                          PFURGBBHAOXLIO-OLQ… C1CC[…  4.88
 4 1,2-Cyclohexanedione                         OILAIQUEIWYQPH-UHF… C1CCC…  5.77
 5 1,3,7-Trimethyluric acid                     BYXCFUMGEBZDDI-UHF… CN1C2…  1.83
 6 1,3 Cyclohexanedione                         HJSLFCCWAKVHIW-UHF… C1CC(…  1.47
 7 1,4-Cyclohexanedicarboxylic acid             PXGZQGDTEZPERC-UHF… C1CC(…  1.56
 8 1,4-Cyclohexanedione                         DCZFGQYXRKMVFG-UHF… C1CC(…  1.15
 9 1,7-Dimethyluric acid                        NOFNCLGCUJJPKU-UHF… CN1C2…  4.09
10 1-Acetylimidazole                            VIHYIVKEECZGOU-UHF… CC(=O…  1.37
# … with 960 more rows
> getCD(HILIC)
Cao-lab-zcmu commented 2 years ago

Unfortunately, even if I use another PC, the error still caused.

> HILIC
# A tibble: 970 × 4
   NAME                                         INCHKEY             SMILES    RT
   <chr>                                        <chr>               <chr>  <dbl>
 1 (2-oxo-2,3-dihydro-1H-indol-3-yl)acetic acid ILGMGHZPXRDCCS-UHF… C1=CC…  2.02
 2 1,1-Dimethyl-4-phenylpiperazinium            WVHNHHJEHFWYHH-UHF… CC1C(…  2.61
 3 1,2-Cyclohexanediol                          PFURGBBHAOXLIO-OLQ… C1CC[…  4.88
 4 1,2-Cyclohexanedione                         OILAIQUEIWYQPH-UHF… C1CCC…  5.77
 5 1,3,7-Trimethyluric acid                     BYXCFUMGEBZDDI-UHF… CN1C2…  1.83
 6 1,3 Cyclohexanedione                         HJSLFCCWAKVHIW-UHF… C1CC(…  1.47
 7 1,4-Cyclohexanedicarboxylic acid             PXGZQGDTEZPERC-UHF… C1CC(…  1.56
 8 1,4-Cyclohexanedione                         DCZFGQYXRKMVFG-UHF… C1CC(…  1.15
 9 1,7-Dimethyluric acid                        NOFNCLGCUJJPKU-UHF… CN1C2…  4.09
10 1-Acetylimidazole                            VIHYIVKEECZGOU-UHF… CC(=O…  1.37
# … with 960 more rows

> getCD(HILIC)
...
[1] "965 of 970"
[1] "966 of 970"
[1] "967 of 970"
[1] "968 of 970"
[1] "969 of 970"
[1] "970 of 970"
[1] "Computing Chemical Descriptors 1 of 970 ... Please wait"
Error: segfault from C stack overflow
Warning messages:
1: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
2: In FUN(X[[i]], ...) : The AtomType null could not be found
3: In FUN(X[[i]], ...) : Molecule must have 3D coordinates

And the rcdk package is ok in this machine as well

tobigithub commented 2 years ago

Mmmh, that seems to be similar to this error, which is unfortunately not fixed yet. (https://github.com/PaoloBnn/Retip/issues/3)

T.

kozo2 commented 2 years ago

I am also in trouble with this problem. I can reproduce this with R 4.2.0 in rocker/rstudio Docker image.

[1] "965 of 970"
[1] "966 of 970"
[1] "967 of 970"
[1] "968 of 970"
[1] "969 of 970"
[1] "970 of 970"
[1] "Computing Chemical Descriptors 1 of 970 ... Please wait"
Error: segfault from C stack overflow
Warning messages:
1: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
2: In FUN(X[[i]], ...) : The AtomType null could not be found
3: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
>
kozo2 commented 2 years ago

By the way, this error did not occur on Windows environment. (I got some warnings, but no error occurred.)

[1] "964 of 970"
[1] "965 of 970"
[1] "966 of 970"
[1] "967 of 970"
[1] "968 of 970"
[1] "969 of 970"
[1] "970 of 970"
 50 件以上の警告がありました (最初の 50 個の警告を見るには warnings() を使って下さい) 
> warnings()
 警告メッセージ: 
1: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
2: In FUN(X[[i]], ...) : The AtomType null could not be found
3: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
4: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
5: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
6: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
7: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
8: In FUN(X[[i]], ...) : The AtomType null could not be found
9: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
10: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
11: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
12: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
13: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
14: In FUN(X[[i]], ...) : The AtomType null could not be found
15: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
16: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
17: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
18: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
19: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
20: In FUN(X[[i]], ...) : The AtomType null could not be found
21: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
22: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
23: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
24: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
25: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
26: In FUN(X[[i]], ...) : The AtomType null could not be found
27: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
28: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
29: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
30: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
31: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
32: In FUN(X[[i]], ...) : The AtomType null could not be found
33: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
34: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
35: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
36: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
37: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
38: In FUN(X[[i]], ...) : The AtomType null could not be found
39: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
40: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
41: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
42: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
43: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
44: In FUN(X[[i]], ...) : The AtomType null could not be found
45: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
46: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
47: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
48: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
49: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
50: In FUN(X[[i]], ...) : The AtomType null could not be found
>