gitter.demo() warnings

[sathishksrinivasan]

I am getting plenty of warning messages while running gitter.demo() command. Please see below. Sathish

gitter.demo() Processing sample.jpg ... |======================================================================================| 100%

gitter v1.0.3 data file

Function call: gitter(image.file = f, verbose = "p") Elapsed time: 5.63 secs Plate format: 32 x 48 (1536) Colony size statistics: Min. 1st Qu. Median Mean 3rd Qu. Max. 0.0 196.8 303.0 262.7 356.0 670.0 Dat file (first 6 rows): row col size circularity flags 1 1 1 357 0.5387 C 2 1 2 160 0.8029
3 1 3 393 0.8130
4 1 4 378 0.4710 C 5 1 5 261 0.1836 C 6 1 6 389 0.1588 S,C Plate warnings: high count of small colony sizes, high count of low colony circularity There were 50 or more warnings (use warnings() to see the first 50)

warnings() Warning messages: 1: In cor(ref, z, method = "spearman") : the standard deviation is zero 2: In cor(ref, z, method = "spearman") : the standard deviation is zero 3: In cor(ref, z, method = "spearman") : the standard deviation is zero 4: In cor(ref, z, method = "spearman") : the standard deviation is zero 5: In cor(ref, z, method = "spearman") : the standard deviation is zero 6: In cor(ref, z, method = "spearman") : the standard deviation is zero 7: In cor(ref, z, method = "spearman") : the standard deviation is zero 8: In cor(ref, z, method = "spearman") : the standard deviation is zero 9: In cor(ref, z, method = "spearman") : the standard deviation is zero 10: In cor(ref, z, method = "spearman") : the standard deviation is zero 11: In cor(ref, z, method = "spearman") : the standard deviation is zero 12: In cor(ref, z, method = "spearman") : the standard deviation is zero 13: In cor(ref, z, method = "spearman") : the standard deviation is zero 14: In cor(ref, z, method = "spearman") : the standard deviation is zero 15: In cor(ref, z, method = "spearman") : the standard deviation is zero 16: In cor(ref, z, method = "spearman") : the standard deviation is zero 17: In cor(ref, z, method = "spearman") : the standard deviation is zero 18: In cor(ref, z, method = "spearman") : the standard deviation is zero 19: In cor(ref, z, method = "spearman") : the standard deviation is zero 20: In cor(ref, z, method = "spearman") : the standard deviation is zero 21: In cor(ref, z, method = "spearman") : the standard deviation is zero 22: In cor(ref, z, method = "spearman") : the standard deviation is zero 23: In cor(ref, z, method = "spearman") : the standard deviation is zero 24: In cor(ref, z, method = "spearman") : the standard deviation is zero 25: In cor(ref, z, method = "spearman") : the standard deviation is zero 26: In cor(ref, z, method = "spearman") : the standard deviation is zero 27: In cor(ref, z, method = "spearman") : the standard deviation is zero 28: In cor(ref, z, method = "spearman") : the standard deviation is zero 29: In cor(ref, z, method = "spearman") : the standard deviation is zero 30: In cor(ref, z, method = "spearman") : the standard deviation is zero 31: In cor(ref, z, method = "spearman") : the standard deviation is zero 32: In cor(ref, z, method = "spearman") : the standard deviation is zero 33: In cor(ref, z, method = "spearman") : the standard deviation is zero 34: In cor(ref, z, method = "spearman") : the standard deviation is zero 35: In cor(ref, z, method = "spearman") : the standard deviation is zero 36: In cor(ref, z, method = "spearman") : the standard deviation is zero 37: In cor(ref, z, method = "spearman") : the standard deviation is zero 38: In cor(ref, z, method = "spearman") : the standard deviation is zero 39: In cor(ref, z, method = "spearman") : the standard deviation is zero 40: In cor(ref, z, method = "spearman") : the standard deviation is zero 41: In cor(ref, z, method = "spearman") : the standard deviation is zero 42: In cor(ref, z, method = "spearman") : the standard deviation is zero 43: In cor(ref, z, method = "spearman") : the standard deviation is zero 44: In cor(ref, z, method = "spearman") : the standard deviation is zero 45: In cor(ref, z, method = "spearman") : the standard deviation is zero 46: In cor(ref, z, method = "spearman") : the standard deviation is zero 47: In cor(ref, z, method = "spearman") : the standard deviation is zero 48: In cor(ref, z, method = "spearman") : the standard deviation is zero 49: In cor(ref, z, method = "spearman") : the standard deviation is zero 50: In cor(ref, z, method = "spearman") : the standard deviation is zero

sessionInfo() R version 3.1.2 (2014-10-31) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] gitter_1.0.4 loaded via a namespace (and not attached): [1] abind_1.4-0 BiocGenerics_0.12.1 colorspace_1.2-4 digest_0.6.8
[5] EBImage_4.8.3 ggplot2_1.0.0 grid_3.1.2 gtable_0.1.2
[9] jpeg_0.1-8 labeling_0.3 lattice_0.20-29 locfit_1.5-9.1
[13] logging_0.7-103 MASS_7.3-35 munsell_0.4.2 parallel_3.1.2
[17] PET_0.4.9 plyr_1.8.1 png_0.1-7 proto_0.3-10
[21] Rcpp_0.11.3 reshape2_1.4.1 scales_0.2.4 stringr_0.6.2
[25] tiff_0.1-5 tools_3.1.2

[omarwagih]

Those occur when computing the correlation profiles, when vectors have zero variance (e.g. stretch of zeros). You can safely ignore them, the warnings will not affect your results. The warnings will be suppressed in the next update.

Thanks

On 25 Mar 2015, at 20:00, sathishksrinivasan notifications@github.com wrote:

I am getting plenty of warning messages while running gitter.demo() command. Please see below. Sathish

gitter.demo() Processing sample.jpg ... |======================================================================================| 100%

gitter v1.0.3 data file

Function call: gitter(image.file = f, verbose = "p") Elapsed time: 5.63 secs Plate format: 32 x 48 (1536) Colony size statistics: Min. 1st Qu. Median Mean 3rd Qu. Max. 0.0 196.8 303.0 262.7 356.0 670.0 Dat file (first 6 rows): row col size circularity flags 1 1 1 357 0.5387 C 2 1 2 160 0.8029

3 1 3 393 0.8130

4 1 4 378 0.4710 C 5 1 5 261 0.1836 C 6 1 6 389 0.1588 S,C Plate warnings: high count of small colony sizes, high count of low colony circularity There were 50 or more warnings (use warnings() to see the first 50)

warnings() Warning messages: 1: In cor(ref, z, method = "spearman") : the standard deviation is zero 2: In cor(ref, z, method = "spearman") : the standard deviation is zero 3: In cor(ref, z, method = "spearman") : the standard deviation is zero 4: In cor(ref, z, method = "spearman") : the standard deviation is zero 5: In cor(ref, z, method = "spearman") : the standard deviation is zero 6: In cor(ref, z, method = "spearman") : the standard deviation is zero 7: In cor(ref, z, method = "spearman") : the standard deviation is zero 8: In cor(ref, z, method = "spearman") : the standard deviation is zero 9: In cor(ref, z, method = "spearman") : the standard deviation is zero 10: In cor(ref, z, method = "spearman") : the standard deviation is zero 11: In cor(ref, z, method = "spearman") : the standard deviation is zero 12: In cor(ref, z, method = "spearman") : the standard deviation is zero 13: In cor(ref, z, method = "spearman") : the standard deviation is zero 14: In cor(ref, z, method = "spearman") : the standard deviation is zero 15: In cor(ref, z, method = "spearman") : the standard deviation is zero 16: In cor(ref, z, method = "spearman") : the standard deviation is zero 17: In cor(ref, z, method = "spearman") : the standard deviation is zero 18: In cor(ref, z, method = "spearman") : the standard deviation is zero 19: In cor(ref, z, method = "spearman") : the standard deviation is zero 20: In cor(ref, z, method = "spearman") : the standard deviation is zero 21: In cor(ref, z, method = "spearman") : the standard deviation is zero 22: In cor(ref, z, method = "spearman") : the standard deviation is zero 23: In cor(ref, z, method = "spearman") : the standard deviation is zero 24: In cor(ref, z, method = "spearman") : the standard deviation is zero 25: In cor(ref, z, method = "spearman") : the standard deviation is zero 26: In cor(ref, z, method = "spearman") : the standard deviation is zero 27: In cor(ref, z, method = "spearman") : the standard deviation is zero 28: In cor(ref, z, method = "spearman") : the standard deviation is zero 29: In cor(ref, z, method = "spearman") : the standard deviation is zero 30: In cor(ref, z, method = "spearman") : the standard deviation is zero 31: In cor(ref, z, method = "spearman") : the standard deviation is zero 32: In cor(ref, z, method = "spearman") : the standard deviation is zero 33: In cor(ref, z, method = "spearman") : the standard deviation is zero 34: In cor(ref, z, method = "spearman") : the standard deviation is zero 35: In cor(ref, z, method = "spearman") : the standard deviation is zero 36: In cor(ref, z, method = "spearman") : the standard deviation is zero 37: In cor(ref, z, method = "spearman") : the standard deviation is zero 38: In cor(ref, z, method = "spearman") : the standard deviation is zero 39: In cor(ref, z, method = "spearman") : the standard deviation is zero 40: In cor(ref, z, method = "spearman") : the standard deviation is zero 41: In cor(ref, z, method = "spearman") : the standard deviation is zero 42: In cor(ref, z, method = "spearman") : the standard deviation is zero 43: In cor(ref, z, method = "spearman") : the standard deviation is zero 44: In cor(ref, z, method = "spearman") : the standard deviation is zero 45: In cor(ref, z, method = "spearman") : the standard deviation is zero 46: In cor(ref, z, method = "spearman") : the standard deviation is zero 47: In cor(ref, z, method = "spearman") : the standard deviation is zero 48: In cor(ref, z, method = "spearman") : the standard deviation is zero 49: In cor(ref, z, method = "spearman") : the standard deviation is zero 50: In cor(ref, z, method = "spearman") : the standard deviation is zero

— Reply to this email directly or view it on GitHub https://github.com/omarwagih/gitter/issues/2.

[sathishksrinivasan]

Thanks for the answer.